Molecular Phylogeny of Triticum and Aegilops Genera Based on ITS and MATK Sequence Data

International Nuclear Information System (INIS)

Dizkirici, A.; Kansu, C.; Onde, S.

2016-01-01

Understanding the phylogenetic relationship between Triticum and Aegilops species, which form a vast gene pool of wheat, is very important for breeding new cultivated wheat varieties. In the present study, phylogenetic relationships between Triticum (12 samples from 4 species) and Aegilops (24 samples from 8 species) were investigated using sequences of the nuclear ITS rDNA gene and partial sequences of the matK gene of chloroplast genome. The phylogenetic relationships among species were reconstructed using Maximum Likelihood method. The constructed tree based on the sequences of the nuclear component (ITS) displayed a close relationship between polyploid wheats and Aegilops speltoides species which provided new evidence for the source of the enigmatic B genome donor as Ae. speltoides. Concurrent clustering of Ae. cylindrica and Ae. tauschii and their close positioning to polyploid wheats pointed the source of the D genome as one of these species. As reported before, diploid Triticum species (i.e. T. urartu) were identified as the A genome donors and the positioning of these diploid wheats on the constructed tree are meaningful. The constructed tree based on the chloroplastic matK sequences displayed same relationship between polyploid wheats and Ae. speltoides species providing evidence for the later species being the chloroplast donors for polyploid wheats. Therefore, our results supported the idea of coinheritance of nuclear and chloroplast genomes where Ae. speltoides was the maternal donor. For both trees the remaining Aegilops species produced a distinct cluster whereas with the exception of T. urartu, diploid Triticum species displayed a monophyletic structure. (author)

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

Science.gov (United States)

Budak, Hikmet; Kantar, Melda

2015-07-01

MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

Gametocidal genes of Aegilops: segregation distorters in wheat-Aegilops wide hybridization.

Science.gov (United States)

Niranjana, M

2017-08-01

Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S 1 , S sh , and M g genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

Science.gov (United States)

Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

2015-10-16

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

Contribution of chloroplast DNA in the biodiversity of some Aegilops ...

African Journals Online (AJOL)

Four Aegilops species (Aegilops longissima, Aegilops speltoides, Aegilops searsii and Aegilops caudata) belonging to the family Poaceae were used in this study. Nucleotides of 1651 bp from 5.8 S rRNA gene and the intergenic spacers trnT-trnL and trnL-trnF from the chloroplast DNA were combined together in order to ...

Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

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Moradkhani Hoda

2015-12-01

Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

Ancient hybridizations among the ancestral genomes of bread wheat

Czech Academy of Sciences Publication Activity Database

Marcussen, T.; Sandve, S. R.; Heier, L.; Spannagl, M.; Pfeifer, M.; Rogers, J.; Doležel, Jaroslav; Pozniak, C.; Eversole, K.; Feuillet, C.; Gill, B.; Friebe, B.; Lukaszewski, A.J.; Sourdille, P.; Endo, T. R.; Kubaláková, Marie; Čihalíková, Jarmila; Dubská, Zdeňka; Vrána, Jan; Šperková, Romana; Šimková, Hana; Febrer, M.; Clissold, L.; Jakobsen, K. S.; Wulff, B.H.; Steuernagel, B.; Mayer, K. F. X.; Olsen, O.A.

2014-01-01

Roč. 345, č. 6194 (2014) ISSN 0036-8075 Institutional support: RVO:61389030 Keywords : POLYPLOID WHEAT * HYBRID SPECIATION * AEGILOPS-TAUSCHII Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 33.611, year: 2014

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate ...

Variation in Susceptibility to Wheat dwarf virus among Wild and Domesticated Wheat

Science.gov (United States)

Nygren, Jim; Shad, Nadeem; Kvarnheden, Anders; Westerbergh, Anna

2015-01-01

We investigated the variation in plant response in host-pathogen interactions between wild (Aegilops spp., Triticum spp.) and domesticated wheat (Triticum spp.) and Wheat dwarf virus (WDV). The distribution of WDV and its wild host species overlaps in Western Asia in the Fertile Crescent, suggesting a coevolutionary relationship. Bread wheat originates from a natural hybridization between wild emmer wheat (carrying the A and B genomes) and the wild D genome donor Aegilops tauschii, followed by polyploidization and domestication. We studied whether the strong selection during these evolutionary processes, leading to genetic bottlenecks, may have resulted in a loss of resistance in domesticated wheat. In addition, we investigated whether putative fluctuations in intensity of selection imposed on the host-pathogen interactions have resulted in a variation in susceptibility to WDV. To test our hypotheses we evaluated eighteen wild and domesticated wheat taxa, directly or indirectly involved in wheat evolution, for traits associated with WDV disease such as leaf chlorosis, different growth traits and WDV content. The plants were exposed to viruliferous leafhoppers (Psammotettix alienus) in a greenhouse trial and evaluated at two time points. We found three different plant response patterns: i) continuous reduction in growth over time, ii) weak response at an early stage of plant development but a much stronger response at a later stage, and iii) remission of symptoms over time. Variation in susceptibility may be explained by differences in the intensity of natural selection, shaping the coevolutionary interaction between WDV and the wild relatives. However, genetic bottlenecks during wheat evolution have not had a strong impact on WDV resistance. Further, this study indicates that the variation in susceptibility may be associated with the genome type and that the ancestor Ae. tauschii may be useful as genetic resource for the improvement of WDV resistance in wheat. PMID

Variation in susceptibility to Wheat dwarf virus among wild and domesticated wheat.

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Jim Nygren

Full Text Available We investigated the variation in plant response in host-pathogen interactions between wild (Aegilops spp., Triticum spp. and domesticated wheat (Triticum spp. and Wheat dwarf virus (WDV. The distribution of WDV and its wild host species overlaps in Western Asia in the Fertile Crescent, suggesting a coevolutionary relationship. Bread wheat originates from a natural hybridization between wild emmer wheat (carrying the A and B genomes and the wild D genome donor Aegilops tauschii, followed by polyploidization and domestication. We studied whether the strong selection during these evolutionary processes, leading to genetic bottlenecks, may have resulted in a loss of resistance in domesticated wheat. In addition, we investigated whether putative fluctuations in intensity of selection imposed on the host-pathogen interactions have resulted in a variation in susceptibility to WDV. To test our hypotheses we evaluated eighteen wild and domesticated wheat taxa, directly or indirectly involved in wheat evolution, for traits associated with WDV disease such as leaf chlorosis, different growth traits and WDV content. The plants were exposed to viruliferous leafhoppers (Psammotettix alienus in a greenhouse trial and evaluated at two time points. We found three different plant response patterns: i continuous reduction in growth over time, ii weak response at an early stage of plant development but a much stronger response at a later stage, and iii remission of symptoms over time. Variation in susceptibility may be explained by differences in the intensity of natural selection, shaping the coevolutionary interaction between WDV and the wild relatives. However, genetic bottlenecks during wheat evolution have not had a strong impact on WDV resistance. Further, this study indicates that the variation in susceptibility may be associated with the genome type and that the ancestor Ae. tauschii may be useful as genetic resource for the improvement of WDV resistance in

Breeding value of primary synthetic wheat genotypes for grain yield

Science.gov (United States)

To introduce new genetic diversity into the bread wheat gene pool from its progenitor, Aegilops tauschii (Coss.) Schmalh, 33 primary synthetic hexaploid wheat genotypes (SYN) were crossed to 20 spring bread wheat (BW) cultivars at the International Wheat and Maize Improvement Center. Modified single...

Characterization of a new synthetic wheat – Aegilops biuncialis ...

African Journals Online (AJOL)

The aim of the experiments was to identify the synthetic wheat – Aegilops biuncialis germplasm Line 15-3-2 with 42 chromosomes. Morphologically, the spike of line 15-3-2 is intermediate to those of its wheat and Aegilops parents. Line 15-3-2 displays stable fertility and immunity to wheat powdery mildew and stripe rust.

Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

Czech Academy of Sciences Publication Activity Database

Staňková, Helena; Valárik, Miroslav; Lapitan, N.L.V.; Berkman, P.J.; Batley, J.; Edwards, D.; Luo, M.C.; Tulpová, Zuzana; Kubaláková, Marie; Stein, N.; Doležel, Jaroslav; Šimková, Hana

2015-01-01

Roč. 128, č. 7 (2015), s. 1373-1383 ISSN 0040-5752 R&D Projects: GA ČR(CZ) GAP501/12/2554; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : TRITICUM-AESTIVUM L. * BREAD WHEAT * AEGILOPS-TAUSCHII Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.900, year: 2015

Molecular survey of Tamyb10-1 genes and their association with ...

Indian Academy of Sciences (India)

To investigate allelic variation of Myb10-1 genes in Chinese wheat and to examine its association with germination level in wheat, a total of 582 Chinese bread wheat cultivars and 110 Aegilops tauschii accessions were used to identify allelic variations of three Myb10-1 genes. Identification results indicated that there is a ...

Accelerated Senescence and Enhanced Disease Resistance in Hybrid Chlorosis Lines Derived from Interspecific Crosses between Tetraploid Wheat and Aegilops tauschii

Science.gov (United States)

Tosa, Yukio; Yoshida, Kentaro; Park, Pyoyun; Takumi, Shigeo

2015-01-01

Hybrid chlorosis, a type of hybrid incompatibility, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In a previous study, we reported some types of growth abnormalities such as hybrid necrosis and observed hybrid chlorosis with mild or severe abnormalities in wheat triploids obtained in crosses between tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we compared cytology and gene expression in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis. In addition, we compared disease resistance to wheat blast fungus. In total 55 and 105 genes related to carbohydrate metabolism and 53 and 89 genes for defense responses were markedly up-regulated in the mild and severe chlorosis lines, respectively. Abnormal chloroplasts formed in the mesophyll cells before the leaves yellowed in the hybrid chlorosis lines. The plants with mild chlorosis showed increased resistance to wheat blast and powdery mildew fungi, although significant differences only in two, third internode length and maturation time, out of the examined agricultural traits were found between the wild type and plants showing mild chlorosis. These observations suggest that senescence might be accelerated in hybrid chlorosis lines of wheat synthetics. Moreover, in wheat synthetics showing mild chlorosis, the negative effects on biomass can be minimized, and they may show substantial fitness under pathogen-polluted conditions. PMID:25806790

Accelerated senescence and enhanced disease resistance in hybrid chlorosis lines derived from interspecific crosses between tetraploid wheat and Aegilops tauschii.

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Hiroki Nakano

Full Text Available Hybrid chlorosis, a type of hybrid incompatibility, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In a previous study, we reported some types of growth abnormalities such as hybrid necrosis and observed hybrid chlorosis with mild or severe abnormalities in wheat triploids obtained in crosses between tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we compared cytology and gene expression in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis. In addition, we compared disease resistance to wheat blast fungus. In total 55 and 105 genes related to carbohydrate metabolism and 53 and 89 genes for defense responses were markedly up-regulated in the mild and severe chlorosis lines, respectively. Abnormal chloroplasts formed in the mesophyll cells before the leaves yellowed in the hybrid chlorosis lines. The plants with mild chlorosis showed increased resistance to wheat blast and powdery mildew fungi, although significant differences only in two, third internode length and maturation time, out of the examined agricultural traits were found between the wild type and plants showing mild chlorosis. These observations suggest that senescence might be accelerated in hybrid chlorosis lines of wheat synthetics. Moreover, in wheat synthetics showing mild chlorosis, the negative effects on biomass can be minimized, and they may show substantial fitness under pathogen-polluted conditions.

Spontaneous wheat-Aegilops biuncialis, Ae. geniculata and Ae. triuncialis amphiploid production, a potential way of gene transference

OpenAIRE

Loureiro, I.; Escorial, C.; García-Baudin, J.M.; Chueca, C.

2009-01-01

Some F1 hybrid plants between three species of the Aegilops genus and different hexaploid wheat Triticum aestivum cultivars show certain self-fertility, with averages of F1 hybrids bearing F2 seeds of 8.17%, 5.12% and 48.14% for Aegilops biuncialis, Aegilops geniculata and Aegilops triuncialis respectively. In the Ae. triuncialis-wheat combination with ";Astral" wheat cultivar, the fertility was higher than that found in the other combinations. All the F2 seeds studied were spontaneous amphip...

A large-scale chromosome-specific SNP discovery guideline.

Science.gov (United States)

Akpinar, Bala Ani; Lucas, Stuart; Budak, Hikmet

2017-01-01

Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.

Characterization of a genome-specific Gypsy-like retrotransposon ...

Indian Academy of Sciences (India)

Aegilops ventricosa. As 106. DvDvMvMv. Ae. uniaristata. As136. M. Ae. tauschii. 38. D. T. durum - D. villosum amphipoild. Th1w, Th2w, Th3w, Th1,Th3. ABV. T. aestivum (CS) - D. villorum additional lines. Add. *. 1V-7V. ABDV. *. Add. indicates wheat - D. villosum addition lines. Journal of Genetics, Vol. 92, No. 1, April 2013.

Spontaneous wheat-Aegilops biuncialis, Ae. geniculata and Ae. triuncialis amphiploid production, a potential way of gene transference

Energy Technology Data Exchange (ETDEWEB)

Loureiro, I.; Escorial, C.; Garcia-Baudin, J. M.; Chueca, M. C.

2009-07-01

Some F1 hybrid plants between three species of the Aegilops genus and different hexaploid wheat Triticum aestivum cultivars show certain self-fertility, with averages of F{sub 1} hybrids bearing F{sub 2} seeds of 8.17%, 5.12% and 48.14% for Aegilops biuncialis, Aegilops geniculata and Aegilops triuncialis respectively. In the Ae. triuncialis-wheat combination with Astral wheat cultivar, the fertility was higher than that found in the other combinations. All the F2 seeds studied were spontaneous amphiploids (2n=10x=70). The present study evidences the possibility of spontaneous formation of amphiploids between these three Aegilops species and hexaploid wheat and discusses their relevance for gene transference. Future risk assessment of transgenic wheat cultivars needs to evaluate the importance of amphiploids as a bridge for transgene introgression and for gene escape to the wild. (Author)

Study of improving the quality of bread and wheat-aegilops hybrids with the biotechnological ways

Science.gov (United States)

Ganbarzada, Aygun; Hasanova, Sudaba

2016-08-01

The great need of the people to bread demands to increase high qualitative grain plants. At present time for solving these problem different methods of biochemistry, genetics and molecular biology are widely used in the process of selection. To investigate biochemical peculiarities of wheat-aegilops hybrids and to define the correlative relation between these characteristics. To investigate the technological peculiarities of wheat- aegilops hybrids and to define the relation between their main biochemical and technological characteristics. The conclusion of this investigation showed the followings- the wheat-aegilops hybrids according to their morphological and biochemical characteristics have approached to wheats. The electrophoretic spectres of the wheat- aegilops hybrids which have stable for their morphological characteristics are homogeny and heterogenic. Hereditarily some group protein components have passed to their tribes from their parents. But spontaneous hybridisation results in taking part the components of other unknown wheats in these electrophoretic spectres. There is a relation between the electrophoretic spectres and the indications of the grain quality.

An Advanced Backcross Population through Synthetic Octaploid Wheat as a “Bridge”: Development and QTL Detection for Seed Dormancy

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Zhang Dale

2017-12-01

Full Text Available The seed dormancy characteristic is regarded as one of the most critical factors for pre-harvest sprouting (PHS resistance. As a wild wheat relative species, Aegilops tauschii is a potential genetic resource for improving common wheat. In this study, an advanced backcross population (201 strains containing only Ae. tauschii segments was developed by means of synthetic octaploid wheat (hexaploid wheat Zhoumai 18 × Ae. tauschii T093. Subsequently, seed dormancy rate (Dor in the advanced backcross population was evaluated on the day 3, 5 and 7, in which 2 major QTLs (QDor-2D and QDor-3D were observed on chromosomes 2D and 3D with phenotypic variance explained values (PVEs of 10.25 and 20.40%, respectively. Further investigation revealed significant correlation between QDor-3D and Tamyb10 gene, while no association was found between the former and TaVp1 gene, implying that QDor-3D site could be of closer position to Tamyb10. The obtained quantitative trait locus sites (QTLs in this work could be applied to develop wheat cultivars with PHS resistance.

Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat

Czech Academy of Sciences Publication Activity Database

Molnár, I.; Vrána, Jan; Burešová, Veronika; Cápal, Petr; Farkas, A.; Darko, E.; Cseh, A.; Kubaláková, Marie; Molnár-Láng, M.; Doležel, Jaroslav

2016-01-01

Roč. 88, č. 3 (2016), s. 452-467 ISSN 0960-7412 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : tertiary gene pool * triticum-aestivum * common wheat * addition lines * mitotic chromosomes * plant chromosomes * hexaploid wheat * ae. speltoides * dna-sequences * rye genome * Aegilops umbellulata * Aegilops comosa * Aegilops speltoides * Aegilops markgrafii * flow cytometric chromosome sorting * fluorescence insitu hybridization * conserved orthologous set markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.901, year: 2016

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Czech Academy of Sciences Publication Activity Database

Mayer, K. F. X.; Rogers, J.; Doležel, Jaroslav; Pozniak, C.; Feuillet, C.; Lukaszewski, A.J.; Sourdille, P.; Kubaláková, Marie; Čihalíková, Jarmila; Dubská, Zdeňka; Vrána, Jan; Šperková, Romana; Šimková, Hana; Choulet, F.; Stein, N.; Praud, S.

2014-01-01

Roč. 345, č. 6194 (2014) ISSN 0036-8075 R&D Projects: GA ČR GBP501/12/G090; GA ČR(CZ) GAP501/12/2554; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : GENE-EXPRESSION * POLYPLOID WHEAT * AEGILOPS-TAUSCHII Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 33.611, year: 2014 http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=CCC&DestLinkType=FullRecord&UT=000339400700040

Mapping of stripe rust resistance gene in an Aegilops caudata ...

Indian Academy of Sciences (India)

PUNEET INDER TOOR

A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated .... infector rows and experimental material with the mixture of uredinospores of Pst ...

Variations and classification of toxic epitopes related to celiac disease among α-gliadin genes from four Aegilops genomes.

Science.gov (United States)

Li, Jie; Wang, Shunli; Li, Shanshan; Ge, Pei; Li, Xiaohui; Ma, Wujun; Zeller, F J; Hsam, Sai L K; Yan, Yueming

2012-07-01

The α-gliadins are associated with human celiac disease. A total of 23 noninterrupted full open reading frame α-gliadin genes and 19 pseudogenes were cloned and sequenced from C, M, N, and U genomes of four diploid Aegilops species. Sequence comparison of α-gliadin genes from Aegilops and Triticum species demonstrated an existence of extensive allelic variations in Gli-2 loci of the four Aegilops genomes. Specific structural features were found including the compositions and variations of two polyglutamine domains (QI and QII) and four T cell stimulatory toxic epitopes. The mean numbers of glutamine residues in the QI domain in C and N genomes and the QII domain in C, N, and U genomes were much higher than those in Triticum genomes, and the QI domain in C and N genomes and the QII domain in C, M, N, and U genomes displayed greater length variations. Interestingly, the types and numbers of four T cell stimulatory toxic epitopes in α-gliadins from the four Aegilops genomes were significantly less than those from Triticum A, B, D, and their progenitor genomes. Relationships between the structural variations of the two polyglutamine domains and the distributions of four T cell stimulatory toxic epitopes were found, resulting in the α-gliadin genes from the Aegilops and Triticum genomes to be classified into three groups.

Isolation and characterization of an isoamylase gene from rye

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Ke Zheng

2013-12-01

Full Text Available Genomic DNA and cDNA sequences of an isoamylase gene were isolated and characterized from the rye genome. The full-lengths of the rye isoamylase gene are 7351 bp for genomic DNA and 2364 bp for cDNA. There are 18 exons and 17 introns in the genomic sequence, which shares a similar organization with homologous genes from Aegilops tauschii, maize, rice and Arabidopsis. Exon regions of rye and other plant isoamylase genes are more conserved than the introns. High sequence similarity (> 95% was observed in mature proteins of isoamylase genes originating from rye, Ae. tauschii, wheat and barley. The transcript profile revealed that rye isoamylase is mainly expressed in the seed endosperm with a maximum level at the middle developmental stage (15 DPA. A phylogenetic tree based on the deduced aa sequences of mature proteins from rye and other plant isoamylases indicated that rye isoamylase is more closely related to Ae. tauschii wDBE1 and wheat iso1. This is the first report on identification and characterization of the isoamylase gene from rye, making it possible to explore the roles of this enzyme for amylopectin development in rye and triticale.

Contribution of chloroplast DNA in the biodiversity of some Aegilops ...

African Journals Online (AJOL)

user

2011-03-21

Mar 21, 2011 ... caudata) belonging to the family Poaceae were used in this study. Nucleotides of 1651 ... terranean basin and grow well in the high rainy areas. Syria is ... ate and easy identification of Aegilops species is required. Molecular ...

Addition of Aegilops U and M Chromosomes Affects Protein and Dietary Fiber Content of Wholemeal Wheat Flour

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Marianna Rakszegi

2017-09-01

Full Text Available Cereal grain fiber is an important health-promoting component in the human diet. One option to improve dietary fiber content and composition in wheat is to introduce genes from its wild relatives Aegilops biuncialis and Aegilops geniculata. This study showed that the addition of chromosomes 2Ug, 4Ug, 5Ug, 7Ug, 2Mg, 5Mg, and 7Mg of Ae. geniculata and 3Ub, 2Mb, 3Mb, and 7Mb of Ae. biuncialis into bread wheat increased the seed protein content. Chromosomes 1Ug and 1Mg increased the proportion of polymeric glutenin proteins, while the addition of chromosomes 1Ub and 6Ub led to its decrease. Both Aegilops species had higher proportions of β-glucan compared to arabinoxylan (AX than wheat lines, and elevated β-glucan content was also observed in wheat chromosome addition lines 5U, 7U, and 7M. The AX content in wheat was increased by the addition of chromosomes 5Ug, 7Ug, and 1Ub while water-soluble AX was increased by the addition of chromosomes 5U, 5M, and 7M, and to a lesser extent by chromosomes 3, 4, 6Ug, and 2Mb. Chromosomes 5Ug and 7Mb also affected the structure of wheat AX, as shown by the pattern of oligosaccharides released by digestion with endoxylanase. These results will help to map genomic regions responsible for edible fiber content in Aegilops and will contribute to the efficient transfer of wild alleles in introgression breeding programs to obtain wheat varieties with improved health benefits.Key Message: Addition of Aegilops U- and M-genome chromosomes 5 and 7 improves seed protein and fiber content and composition in wheat.

Transfer of stripe rust resistance from Aegilops variabilis to bread ...

African Journals Online (AJOL)

In terms of area, the bread wheat producing regions of China comprise the largest area in the world that is constantly threatened by stripe rust epidemics. Consequently, it is important to exploit new adultplant resistance genes in breeding. This study reports the transfer of stripe rust resistance from Aegilops variabilis to ...

Species variation of Aegilops genus and heavy metal content in plant habitat soil at southern Adriatic localities

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Dimitrijević Miodrag

2014-01-01

Full Text Available The Aegilops genus is a wild relative to the bread wheat, having chromosomes homologous to wheat chromosomes. That genus could be the source of many usefull abiotic stress tolerance genes. Facing a global climate changes, as well as, environmental erosion, it is important to create a desirable genetic variability that could correspond to environmental challenges. Heavy metals in soil could cause soil pollution, could lead to different phenotypic changes in plants, and could enter food chain. Assessment of Aegilops sp. population variation, as well as, heavy metal content in their habitat was the main goal in this research. Aegilops population composition was examined and samples were taken from 55 localities of South Adriatic coastal and littoral areas. Topsoil samples from all the localities were taken and heavy metal content, namely Cr, Pb, Zn, Ni, Cd and Cu, was analyzed,. Manganese content was measured, as well. Value of pH was established.

Still under the ancestors' shadow? Ancestor worship and family formation in contemporary China

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Anning Hu

2018-01-01

Full Text Available Background: Ancestor worship in China used to be an indispensable component of marriage and family life because it fostered an orientation toward perpetuating the family line. However, whether or not ancestor worship still matters in contemporary China is an open question. Objective: This article presents a comprehensive study of the association between ancestor worship practices and 1 the timing of transition to first marriage, 2 the pattern of childbearing, and 3 the orientation toward son preference. Methods: Drawing on the adult sample from the Chinese Family Panel Studies 2010, several multivariate models (Cox proportional hazard model, probit regression model, negative binomial regression models, and ordered probit model were fitted, corresponding to different types of outcome. Results: All else being equal, involvement in ancestor worship practices is correlated with 1 an early transition to marriage, 2 a larger number of children, 3 a higher probability of having at least one son, and 4 a larger number of sons. Conclusions: The relevance of the kinship tradition to family formation persists in contemporary China and has not faded away. Contribution: By highlighting the demographic implications of ancestor worship, this study illustrates the ongoing connection between culture and demography.

Transfer of HMW glutenin subunits from Aegilops kotschyi to wheat through radiation hybridization

International Nuclear Information System (INIS)

Singh, Jasmeet; Sheikh, Imran; Sharma, Prachi

2016-01-01

High molecular weight glutenin subunits (HMWGS) are responsible for dough elasticity and bread making quality of bread wheat. Related wild non-progenitor species, Aegilops kotschyi possesses higher molecular weight x and y glutenin subunits than the bread wheat cultivars. A wheat-Aegilops substitution line with 1U chromosome was used for the transfer of (HMWGS) of 1U to wheat by using pollen radiation hybridization approach. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiling showed different patterns of allelic variations with either the presence or absence of HMWGS, Glu-1A (1, null), Glu-1B (7, 7 + 8, 17 + 18) and Glu-1D (5 + 10, 2 + 12, null). The pollen irradiated wheat-Aegilops derivatives, B-56-1-4-2, B-56-1-4-3, B-14-1 and B-14-2 with Glu1Ux and 1Uy and absence or presence of some Glu-1A and Glu-1B HMWGS showed high micro SDS sedimentation test (MST) values while B-16-1 and B-16-2 had moderate MST values and high protein content. However, B-58-3 with transfer of Glu-1Ux + 1Uy for Glu-1D showed very low MST values indicating that Glu-1Ux + 1Uy enhance MST value only in the presence of Glu1D HMWGS. The transfer/substitution of alien HMW-GS for Glu-1A and or Glu-1B loci only can lead to improved bread making quality of wheat. (author)

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size.

Science.gov (United States)

Dvorak, Jan; Wang, Le; Zhu, Tingting; Jorgensen, Chad M; Deal, Karin R; Dai, Xiongtao; Dawson, Matthew W; Müller, Hans-Georg; Luo, Ming-Cheng; Ramasamy, Ramesh K; Dehghani, Hamid; Gu, Yong Q; Gill, Bikram S; Distelfeld, Assaf; Devos, Katrien M; Qi, Peng; You, Frank M; Gulick, Patrick J; McGuire, Patrick E

2018-05-16

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum, and rice. Similar searches were initiated with genes annotated in the rice pseudomolecules. Matrices of colinear genes and rearrangements in their order were constructed. Optical Bionano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of colinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene colinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon, and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 colinear genes. The rates of acquisition of major rearrangements were greater in the wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice, and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit caused the fast evolution of the Triticeae genomes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Wheat-specific gene, ribosomal protein l21, used as the endogenous reference gene for qualitative and real-time quantitative polymerase chain reaction detection of transgenes.

Science.gov (United States)

Liu, Yi-Ke; Li, He-Ping; Huang, Tao; Cheng, Wei; Gao, Chun-Sheng; Zuo, Dong-Yun; Zhao, Zheng-Xi; Liao, Yu-Cai

2014-10-29

Wheat-specific ribosomal protein L21 (RPL21) is an endogenous reference gene suitable for genetically modified (GM) wheat identification. This taxon-specific RPL21 sequence displayed high homogeneity in different wheat varieties. Southern blots revealed 1 or 3 copies, and sequence analyses showed one amplicon in common wheat. Combined analyses with sequences from common wheat (AABBDD) and three diploid ancestral species, Triticum urartu (AA), Aegilops speltoides (BB), and Aegilops tauschii (DD), demonstrated the presence of this amplicon in the AA genome. Using conventional qualitative polymerase chain reaction (PCR), the limit of detection was 2 copies of wheat haploid genome per reaction. In the quantitative real-time PCR assay, limits of detection and quantification were about 2 and 8 haploid genome copies, respectively, the latter of which is 2.5-4-fold lower than other reported wheat endogenous reference genes. Construct-specific PCR assays were developed using RPL21 as an endogenous reference gene, and as little as 0.5% of GM wheat contents containing Arabidopsis NPR1 were properly quantified.

Study of the repeatability of histone genes in the ploidy series of wheat and Aegilops

International Nuclear Information System (INIS)

Vakhitov, V.A.; Kulikov, A.M.

1986-01-01

The hDNA content and number of histone genes in the genomes of different wheat and Aegilops species have been determined by molecular hybridization of DNA with 125 I-histone DNA of Drosophila (L-repeat) on nitrocellulose filters. It has been demonstrated that the proportion of hDNA in the total DNA of diploid and polyploid wheat species is (1.3-7.7) x 10 -3 % (57-850 genes), and in the ploidy series of Aegilops species (2.0-8.0) x 10 -3 % (89-780 genes). The repeatability of the histone genes generally increases at each ploidy level in the species with higher DNA content. At the same time, it has been demonstrated that the DNA content is not the only factor determining repeatability of the histone genes, as some diploid and allopolyploid species have similar number of these genes. It has been concluded that genetic mechanisms are involved in the regulation of the number of histone genes

Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

Czech Academy of Sciences Publication Activity Database

Koo, D.H.; Tiwari, V.K.; Hřibová, Eva; Doležel, Jaroslav; Friebe, B.; Gill, B.S.

2016-01-01

Roč. 148, č. 4 (2016), s. 314-321 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : in-situ hybridization * chromosome addition lines * resistance genes lr57 * repetitive dna * triticum-ovatum * powdery mildew * plant genome * bread wheat * leaf rust * identification * Aegilops geniculata * Chromosome identification * Fluorescence in situ hybridization * Satellite DNA * Wheat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata.

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István Molnár

Full Text Available This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii

Czech Academy of Sciences Publication Activity Database

Molnár, I.; Kubaláková, Marie; Šimková, Hana; Farkas, A.; Cseh, A.; Megyeri, M.; Vrána, Jan; Molnár-Láng, M.; Doležel, Jaroslav

2014-01-01

Roč. 127, č. 5 (2014), s. 1091-1104 ISSN 0040-5752 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional support: RVO:61389030 Keywords : SYNTHETIC HEXAPLOID WHEAT * AEGILOPS-TRITICUM GROUP * GENETIC-LINKAGE MAP Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.790, year: 2014

Inheritance of Protein Patterns in a Synthetic Allopolyploid of Triticum Monococcum (AA) and Aegilops Ventricosa (DDMvMv)

DEFF Research Database (Denmark)

Siddiqui, K. A.; Ingversen, J.; Køie, B.

1972-01-01

Patterns of seed proteins in Triticum monococcum (2n = 2x = 14 = AA), Aegilops ventricosa (2n = 4x = 28 = DDMVMV), and their synthetic amphiploid were studied. The distribution of proteins in the individual Osborne protein fractions of the amphiploid was characterized by a 14 per cent increase...

Genetic Diversity of Aegilops cylindrica Species from West of Iran Using Morphological and Phenological Traits

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M. Arabbeigi

2015-12-01

Full Text Available Aegilops cylindrica species (CCDD, 2n = 4x = 28 is one of the wild relatives of wheat and hence known as a valuable source of genes related to biotic and abiotic stress tolerance. In this study genetic variation of 66 Aegilops cylindrica genotypes collected from west and northwestern of Iran was evaluated using quantitative and qualitative morphological traits. The results indicated that glumelle (lemma length and glume color traits had the highest variation as the quantitative and qualitative traits, respectively. The principal components analysis (PCA indicated 6 components that first component justified %30.3 total variation. Flag leaf color and fluffiness had the highest contribution in this component and thus the first component named as the flag leaf component. The cluster analysis divided the studied genotypes into three groups.  Genotypes originating from west of Iran were included in the first group and genotypes from northwestern Iran were clustered into the second and third groups. It could be concluded that the high genetic variation among genotypes of Ae. cylindrica revealed in this study can be utilized to improve wheat particularly for tolerance to biotic and abiotic stresses.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

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McGuire Patrick E

2010-12-01

Full Text Available Abstract Background A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. Results Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. Conclusions In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large

Random ancestor trees

International Nuclear Information System (INIS)

Ben-Naim, E; Krapivsky, P L

2010-01-01

We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

Near-optimal labeling schemes for nearest common ancestors

DEFF Research Database (Denmark)

Alstrup, Stephen; Bistrup Halvorsen, Esben; Larsen, Kasper Green

2014-01-01

and Korman (STOC'10) established that labels in ancestor labeling schemes have size log n + Θ(log log n), our new lower bound separates ancestor and NCA labeling schemes. Our upper bound improves the 10 log n upper bound by Alstrup, Gavoille, Kaplan and Rauhe (TOCS'04), and our theoretical result even...

Addition of aegilops U and M chromosomes affects protein and dietary fiber content of wholemeal wheat flour

Czech Academy of Sciences Publication Activity Database

Rakszegi, M.; Molnár, I.; Lovegrove, A.; Darkó, É.; Farkas, A.; Láng, L.; Bedő, Z.; Doležel, Jaroslav; Molnár-Láng, M.; Shewry, P.

2017-01-01

Roč. 8, SEP 6 (2017), č. článku 1529. ISSN 1664-462X R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Aegilops * Arabinoxylan * Dietary fiber * U and M genomes * Wheat * β-glucan Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 4.298, year: 2016

Dewey Called Them Utopians, I Call Them Ancestors

Science.gov (United States)

Kulago, Hollie A.

2018-01-01

In this article, I will describe how the Utopians whom John Dewey once referenced are possibly the ancestors of Indigenous peoples, in this case, ancestors of the Diné. I will describe a Diné philosophy of education through the Kinaaldá ceremony which was the first ceremony created by the Holy People of the Diné to ensure the survival of the…

THE WHITE BLOOD ANCESTOR?

OpenAIRE

M.Arulmani; V.R.Hema Latha

2014-01-01

This scientific research article focus that “Red colour blood” of human shall be considered as the 3rd generation Blood and the Human on origin shall be considered having white colour Blood. The white colour blood of human Ancestor shall be considered composed of only ions of Photon, Electron, Proton and free from Hydrogen, Carbon, Nitrogen, Ozone.

Proposed Ancestors of Phage Nucleic Acid Packaging Motors (and Cells

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Philip Serwer

2011-07-01

Full Text Available I present a hypothesis that begins with the proposal that abiotic ancestors of phage RNA and DNA packaging systems (and cells include mobile shells with an internal, molecule-transporting cavity. The foundations of this hypothesis include the conjecture that current nucleic acid packaging systems have imprints from abiotic ancestors. The abiotic shells (1 initially imbibe and later also bind and transport organic molecules, thereby providing a means for producing molecular interactions that are links in the chain of events that produces ancestors to the first molecules that are both information carrying and enzymatically active, and (2 are subsequently scaffolds on which proteins assemble to form ancestors common to both shells of viral capsids and cell membranes. Emergence of cells occurs via aggregation and merger of shells and internal contents. The hypothesis continues by using proposed imprints of abiotic and biotic ancestors to deduce an ancestral thermal ratchet-based DNA packaging motor that subsequently evolves to integrate a DNA packaging ATPase that provides a power stroke.

Determination of the number of copies of genes coding for 5s-rRNA and tRNA in the genomes of 43 species of wheat and Aegilops

International Nuclear Information System (INIS)

Vakhitov, V.A.; Gimalov, F.R.; Nikonorov, Yu.M.

1986-01-01

The number of 5s-rRNA and tRNA genes has been studied in 43 species of wheat and Aegilops differing in ploidy level, genomic composition and origin. It has been demonstrated that the repeatability of the 5s-rRNA and tRNA genes increases in wheat with increasing ploidy level, but not in proportion to the genome size. In Aegilops, in distinction from wheat, the relative as well as absolute number of 5s-RNA genes increases with increasing ploidy level. The proportion of the sequences coding for tRNA in the dipoloid and polyploid Aegilops species is practically similar, while the number of tRNA genes increases almost 2-3 times with increasing ploidy level. Large variability has been recorded between the species with similar genomic composition and ploidy level in respect of the number of the 5s-rRNA and tRNA genes. It has been demonstrated that integration of the initial genomes of the amphidiploids is accompanied by elimination of a particular part of these genomes. It has been concluded that the mechanisms of establishment and evolution of genomes in the intra- and intergeneric allopolyploids are not identical

Interaction of soft wheat Triticum aestivum L. gene ph1b with the Aegilops speltoides Tausch. genotype

Energy Technology Data Exchange (ETDEWEB)

Lapochkina, I.F. [Agricultural Research Institute of Central Non-Chernozem Region, Moscow (Russian Federation)

1995-04-01

It is demonstrated that genotypes of Aegilops speltoides and the phi1b mutant have an additive effect on the level of homeologous chromosome pairing in their F{sub 1} hybrids (2n = 28, ABDS). The contribution of gene ph1b to the total pairing level is 16% and that of the Ae. speltoides genotype is 42%. 9 refs., 1 fig., 2 tabs.

Phylogenetic rooting using minimal ancestor deviation.

Science.gov (United States)

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

The galaxy ancestor problem

Science.gov (United States)

Disney, M. J.; Lang, R. H.

2012-11-01

The Hubble Space Telescope (HST) findsgalaxies whose Tolman dimming exceeds 10 mag. Could evolution alone explain these as our ancestor galaxies or could they be representatives of quite a different dynasty whose descendants are no longer prominent today? We explore the latter hypothesis and argue that surface brightness selection effects naturally bring into focus quite different dynasties from different redshifts. Thus, the HST z = 7 galaxies could be examples of galaxies whose descendants are both too small and too choked with dust to be recognizable in our neighbourhood easily today. Conversely, the ancestors of the Milky Way and its obvious neighbours would have completely sunk below the sky at z > 1.2, unless they were more luminous in the past, although their diffused light could account for the missing re-ionization flux. This Succeeding Prominent Dynasties Hypothesis (SPDH) fits the existing observations both naturally and well even without evolution, including the bizarre distributions of galaxy surface brightness found in deep fields, the angular size ˜(1 + z)-1 law, 'downsizing' which turns out to be an 'illusion' in the sense that it does not imply evolution, 'infant mortality', that is, the discrepancy between stars born and stars seen, the existence of 'red nuggets', and finally the recently discovered and unexpected excess of quasar absorption line damped Lyα systems at high redshift. If galaxies were not significantly brighter in the past and the SPDH were true, then a large proportion of galaxies could remain sunk from sight, possibly at all redshifts, and these sunken galaxies could supply the missing re-ionization flux. We show that fishing these sunken galaxies out of the sky by their optical emissions alone is practically impossible, even when they are nearby. More ingenious methods are needed to detect them. It follows that disentangling galaxy evolution through studying ever higher redshift galaxies may be a forlorn hope because one could

Flow sorting of C-genome chromosomes from wild relatives of wheat Aegilops markgrafii, Ae. triuncialis and Ae. cylindrica, and their molecular organization

Czech Academy of Sciences Publication Activity Database

Molnár, I.; Vrána, Jan; Farkas, A.; Kubaláková, Marie; Cseh, A.; Molnár-Láng, M.; Doležel, Jaroslav

2015-01-01

Roč. 116, č. 2 (2015), s. 189-200 ISSN 0305-7364 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Aegilops markgrafii * Ae. triuncialis * Ae. cylindrica Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.982, year: 2015

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies.

Science.gov (United States)

Tulpová, Zuzana; Luo, Ming-Cheng; Toegelová, Helena; Visendi, Paul; Hayashi, Satomi; Vojta, Petr; Paux, Etienne; Kilian, Andrzej; Abrouk, Michaël; Bartoš, Jan; Hajdúch, Marián; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2018-03-08

Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere. Copyright © 2018. Published by Elsevier B.V.

Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis.

Science.gov (United States)

Yu, Guotai; Champouret, Nicolas; Steuernagel, Burkhard; Olivera, Pablo D; Simmons, Jamie; Williams, Cole; Johnson, Ryan; Moscou, Matthew J; Hernández-Pinzón, Inmaculada; Green, Phon; Sela, Hanan; Millet, Eitan; Jones, Jonathan D G; Ward, Eric R; Steffenson, Brian J; Wulff, Brande B H

2017-06-01

We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F 6 recombinant inbred line and an F 2 population, two genes were identified that mapped to the short arm of chromosome 1S sh , designated as Sr-1644-1Sh, and the long arm of chromosome 5S sh , designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.

Chromosome Isolation by Flow Sorting in Aegilops umbellulata and Ae. comosa and Their Allotetraploid Hybrids Ae. biuncialis and Ae. geniculata

Czech Academy of Sciences Publication Activity Database

Molnár, I.; Kubaláková, Marie; Šimková, Hana; Cseh, A.; Molnár-Láng, M.; Doležel, Jaroslav

2011-01-01

Roč. 66, č. 11 (2011), s. 1-11 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) LC06004; GA MŠk OC08025 Grant - others:European Regional Development Fund CZ.1.05/2.1.00/ 01.0007 Institutional research plan: CEZ:AV0Z50380511 Keywords : wheat * chromosome isolation * Aegilops umbellulata Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

The Five Ancestors--Book 1: Tiger

Science.gov (United States)

Stone, Jeff

2004-01-01

Losing a job is an awfully low point--until it turns into the opportunity to pursue writing full time, and a book like "The Five Ancestors: Tiger" results. Jeff Stone looks back to his own experience as a young reader and taps that experience to help frame his own writing. An intriguing snapshot of his new book follows.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

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Zhang Li

2012-08-01

Full Text Available Abstract Background A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Results Of the 606 markers used to assemble the genetic map, 588 (97% were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT markers, 72 simple sequence repeat (SSR, one insertion site-based polymorphism (ISBP, and two high-molecular-weight glutenin subunit (HMW-GS markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL, including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. Conclusions A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome.

Science.gov (United States)

Zhang, Li; Luo, Jiang-Tao; Hao, Ming; Zhang, Lian-Quan; Yuan, Zhong-Wei; Yan, Ze-Hong; Liu, Ya-Xi; Zhang, Bo; Liu, Bao-Long; Liu, Chun-Ji; Zhang, Huai-Gang; Zheng, You-Liang; Liu, Deng-Cai

2012-08-13

A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

Information-Theoretic Inference of Common Ancestors

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Bastian Steudel

2015-04-01

Full Text Available A directed acyclic graph (DAG partially represents the conditional independence structure among observations of a system if the local Markov condition holds, that is if every variable is independent of its non-descendants given its parents. In general, there is a whole class of DAGs that represents a given set of conditional independence relations. We are interested in properties of this class that can be derived from observations of a subsystem only. To this end, we prove an information-theoretic inequality that allows for the inference of common ancestors of observed parts in any DAG representing some unknown larger system. More explicitly, we show that a large amount of dependence in terms of mutual information among the observations implies the existence of a common ancestor that distributes this information. Within the causal interpretation of DAGs, our result can be seen as a quantitative extension of Reichenbach’s principle of common cause to more than two variables. Our conclusions are valid also for non-probabilistic observations, such as binary strings, since we state the proof for an axiomatized notion of “mutual information” that includes the stochastic as well as the algorithmic version.

Apparatus Named after Our Academic Ancestors, III

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Greenslade, Thomas B., Jr.

2014-01-01

My academic ancestors in physics have called on me once more to tell you about the apparatus that they devised, and that many of you have used in your demonstrations and labs. This article is about apparatus named after François Arago, Heinrich Helmholtz, Leon Foucault, and James Watt.

Ancestors protocol for scalable key management

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Dieter Gollmann

2010-06-01

Full Text Available Group key management is an important functional building block for secure multicast architecture. Thereby, it has been extensively studied in the literature. The main proposed protocol is Adaptive Clustering for Scalable Group Key Management (ASGK. According to ASGK protocol, the multicast group is divided into clusters, where each cluster consists of areas of members. Each cluster uses its own Traffic Encryption Key (TEK. These clusters are updated periodically depending on the dynamism of the members during the secure session. The modified protocol has been proposed based on ASGK with some modifications to balance the number of affected members and the encryption/decryption overhead with any number of the areas when a member joins or leaves the group. This modified protocol is called Ancestors protocol. According to Ancestors protocol, every area receives the dynamism of the members from its parents. The main objective of the modified protocol is to reduce the number of affected members during the leaving and joining members, then 1 affects n overhead would be reduced. A comparative study has been done between ASGK protocol and the modified protocol. According to the comparative results, it found that the modified protocol is always outperforming the ASGK protocol.

Vacuum fluctuations in an ancestor vacuum: A possible dark energy candidate

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Aoki, Hajime; Iso, Satoshi; Lee, Da-Shin; Sekino, Yasuhiro; Yeh, Chen-Pin

2018-02-01

We consider an open universe created by bubble nucleation, and study possible effects of our "ancestor vacuum," a de Sitter space in which bubble nucleation occurred, on the present universe. We compute vacuum expectation values of the energy-momentum tensor for a minimally coupled scalar field, carefully taking into account the effect of the ancestor vacuum by the Euclidean prescription. We pay particular attention to the so-called supercurvature mode, a non-normalizable mode on a spatial slice of the open universe, which has been known to exist for sufficiently light fields. This mode decays in time most slowly, and may leave residual effects of the ancestor vacuum, potentially observable in the present universe. We point out that the vacuum energy of the quantum field can be regarded as dark energy if mass of the field is of order the present Hubble parameter or smaller. We obtain preliminary results for the dark energy equation of state w (z ) as a function of the redshift.

Allocation of the S-genome chromosomes of Aegilops variabilis Eig. carrying powdery mildew resistance in triticale (× Triticosecale Wittmack).

Science.gov (United States)

Kwiatek, M; Belter, J; Majka, M; Wiśniewska, H

2016-03-01

It has been hypothesized that the powdery mildew adult plant resistance (APR) controlled by the Pm13 gene in Aegilops longissima Schweinf. & Muschl. (S(l)S(l)) has been evolutionary transferred to Aegilops variabilis Eig. (UUSS). The molecular marker analysis and the visual evaluation of powdery mildew symptoms in Ae. variabilis and the Ae. variabilis × Secale cereale amphiploid forms (2n = 6x = 42, UUSSRR) showed the presence of product that corresponded to Pm13 marker and the lower infection level compared to susceptible model, respectively. This study also describes the transfer of Ae. variabilis Eig. (2n = 4x = 28, U(v)U(v)S(v)S(v)) chromosomes, carrying powdery mildew resistance, into triticale (× Triticosecale Wittm., 2n = 6x = 42, AABBRR) using Ae. variabilis × S. cereale amphiploid forms. The individual chromosomes of Ae. variabilis, triticale 'Lamberto' and hybrids were characterized by genomic and fluorescence in situ hybridization (GISH/FISH). The chromosome configurations of obtained hybrid forms were studied at first metaphase of meiosis of pollen mother cells (PMCs) using GISH. The statistical analysis showed that the way of S-genome chromosome pairing and transmission to subsequent hybrid generations was diploid-like and had no influence on chromosome pairing of triticale chromosomes. The cytogenetic study of hybrid forms were supported by the marker-assisted selection using Pm13 marker and visual evaluation of natural infection by Blumeria graminis, that allowed to select the addition or substitution lines of hybrids carrying chromosome 3S(v) which were tolerant to the powdery mildew infection.

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

DEFF Research Database (Denmark)

Seberg, Ole; Frederiksen, Signe Elisabeth

2001-01-01

not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx....... 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally...... parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent....

Tapetal-Delayed Programmed Cell Death (PCD and Oxidative Stress-Induced Male Sterility of Aegilops uniaristata Cytoplasm in Wheat

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Zihan Liu

2018-06-01

Full Text Available Cytoplasmic male sterility (CMS plays a crucial role in the utilization of hybrid vigor. Pollen development is often accompanied by oxidative metabolism responses and tapetal programmed cell death (PCD, and deficiency in these processes could lead to male sterility. Aegilops uniaristata cytoplasmic male sterility (Mu-CMS wheat is a novel male-sterile line in wheat, which possess important potential in hybrid wheat breeding. However, its CMS mechanisms remain poorly understood. In our study, U87B1-706A, with the Aegilops uniaristata cytoplasm, and the maintainer line 706B were used to explore the abortive reason. Compared with 706B, histological analysis and PCD detection of the anther demonstrated that U87B1-706A appeared as delayed tapetal PCD as well as a disorganized organelle phenotype in the early uninucleate stage. Subsequently, a shrunken microspore and disordered exine structure were exhibited in the late uninucleate stage. While the activities of antioxidase increased markedly, the nonenzymatic antioxidant contents declined obviously following overacummulation of reactive oxygen species (ROS during pollen development in U87B1-706A. Real-time quantitative PCR testified that the transcript levels of the superoxide dismutase (SOD, catalase (CAT, and ascorbate peroxidase (APX genes, encoding pivotal antioxidant enzymes, were up-regulated in early pollen development. Therefore, we deduce excess ROS as a signal may be related to the increased expression levels of enzyme genes, thereby breaking the antioxidative system balance, resulting in delayed tapetal PCD initiation, which finally led to pollen abortion and male sterility in U87B1-706A. These results provide evidence to further explore the mechanisms of abortive pollen in CMS wheat.

Mapping of powdery mildew resistance gene Pm53 introgressed from Aegilops speltoides into soft red winter wheat.

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Petersen, Stine; Lyerly, Jeanette H; Worthington, Margaret L; Parks, Wesley R; Cowger, Christina; Marshall, David S; Brown-Guedira, Gina; Murphy, J Paul

2015-02-01

A powdery mildew resistance gene was introgressed from Aegilops speltoides into winter wheat and mapped to chromosome 5BL. Closely linked markers will permit marker-assisted selection for the resistance gene. Powdery mildew of wheat (Triticum aestivum L.) is a major fungal disease in many areas of the world, caused by Blumeria graminis f. sp. tritici (Bgt). Host plant resistance is the preferred form of disease prevention because it is both economical and environmentally sound. Identification of new resistance sources and closely linked markers enable breeders to utilize these new sources in marker-assisted selection as well as in gene pyramiding. Aegilops speltoides (2n = 2x = 14, genome SS), has been a valuable disease resistance donor. The powdery mildew resistant wheat germplasm line NC09BGTS16 (NC-S16) was developed by backcrossing an Ae. speltoides accession, TAU829, to the susceptible soft red winter wheat cultivar 'Saluda'. NC-S16 was crossed to the susceptible cultivar 'Coker 68-15' to develop F2:3 families for gene mapping. Greenhouse and field evaluations of these F2:3 families indicated that a single gene, designated Pm53, conferred resistance to powdery mildew. Bulked segregant analysis showed that multiple simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers specific to chromosome 5BL segregated with the resistance gene. The gene was flanked by markers Xgwm499, Xwmc759, IWA6024 (0.7 cM proximal) and IWA2454 (1.8 cM distal). Pm36, derived from a different wild wheat relative (T. turgidum var. dicoccoides), had previously been mapped to chromosome 5BL in a durum wheat line. Detached leaf tests revealed that NC-S16 and a genotype carrying Pm36 differed in their responses to each of three Bgt isolates. Pm53 therefore appears to be a new source of powdery mildew resistance.

The Ancestor Project: Aboriginal Computer Education through Storytelling

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Weston, Marla; Biin, Dianne

2013-01-01

The goal of the ANCESTOR program is to use digital storytelling as a means of promoting an interest in technology careers for Aboriginal learners, as well as increasing cultural literacy. A curriculum was developed and first tested with Aboriginal students at the LÁU,WELNEW Tribal School near Victoria, British Columbia, Canada. Based on feedback…

The common ancestor of archaea and eukarya was not an archaeon.

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Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

Graves, Ancestors and Cement in Land disputes in Acholi and Ikland, Uganda

DEFF Research Database (Denmark)

Meinert, Lotte; Willerslev, Rane; Seebach, Sophie Hooge

2017-01-01

graves are made concrete and increasingly cemented indices of belonging in wrangles over land. Belonging is often justified through the presence of ancestor graves on land. The cementing of graves turns them into more concrete and durable proofs of ownership, and the reburial of relatives to disputed......The paper explores the roles of graves, ancestors and concrete pillars in disputes over land across different land-systems, -conflicts, and territory making in northern Uganda by comparing extended cases between Acholi in Gulu district and Ik in Kaabong district . In the post-conflict Acholi region...

Potential Implications of Climate Change on Aegilops Species Distribution: Sympatry of These Crop Wild Relatives with the Major European Crop Triticum aestivum and Conservation Issues.

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Ostrowski, Marie-France; Prosperi, Jean-Marie; David, Jacques

2016-01-01

Gene flow from crop to wild relatives is a common phenomenon which can lead to reduced adaptation of the wild relatives to natural ecosystems and/or increased adaptation to agrosystems (weediness). With global warming, wild relative distributions will likely change, thus modifying the width and/or location of co-occurrence zones where crop-wild hybridization events could occur (sympatry). This study investigates current and 2050 projected changes in sympatry levels between cultivated wheat and six of the most common Aegilops species in Europe. Projections were generated using MaxEnt on presence-only data, bioclimatic variables, and considering two migration hypotheses and two 2050 climate scenarios (RCP4.5 and RCP8.5). Overall, a general decline in suitable climatic conditions for Aegilops species outside the European zone and a parallel increase in Europe were predicted. If no migration could occur, the decline was predicted to be more acute outside than within the European zone. The potential sympatry level in Europe by 2050 was predicted to increase at a higher rate than species richness, and most expansions were predicted to occur in three countries, which are currently among the top four wheat producers in Europe: Russia, France and Ukraine. The results are also discussed with regard to conservation issues of these crop wild relatives.

RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

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Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

2007-02-08

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

Alien DNA introgression and wheat DNA rearrangements in a stable wheat line derived from the early generation of distant hybridization.

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Zhang, Lianquan; Liu, Dengcai; Yan, Zehong; Zheng, Youliang

2005-10-01

Polyploidy has been found to be common in plants. Bread or common wheat (Triticum aestivum L., 2n=42) is a good example of allopolyploid made up of three diploid genomes A, B and D. In recent years, by the study of mimicking the origination of common wheat, it was found that changes of DNA sequence and gene expression occurred at the early stages of artificial allohexaploid between tetraploid wheat and Aegilops tauschii, which was probably favorable to genetic diploidization of new synthetic hexaploid wheat. Common wheat 99L2 is a new line stable in genetic, which was derived from the early self-pollinated generation of wide hybrids between common wheat and rye. In this study, it was found that at least two rye DNA segments had been introgressed into 99L2. This result suggested that a mechanism of alien DNA introgression may exist, which was different from the traditional mechanism of chromosome pairing and DNA recombination between wheat and alien species. Meanwhile, during the introgression process of alien rye DNA segments, the changes in DNA sequences of wheat itself occurred.

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

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Patrick Forterre

2013-01-01

Full Text Available It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario. I propose that the ancestors of archaea (and bacteria escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis. Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction could explain why the archaeal and bacterial mobilomes somehow resemble each other.

Cereal cyst nematode resistance conferred by the Cre7 gene from Aegilops triuncialis and its relationship with Cre genes from Australian wheat cultivars

OpenAIRE

Montes, Maria Jesus; Andrés, María Fe; Sin, E.; Lopez Braña, Isidoro; Martín-Sánchez, J.A.; Romero, M.D.; Delibes Castro, Angeles

2008-01-01

Cereal cyst nematode (CCN; Heterodera avenae Woll.) is a root pathogen of cereal crops that can cause severe yield losses in wheat (Triticum aestivum). Differential host–nematode interactions occur in wheat cultivars carrying different CCN resistance (Cre) genes. The objective of this study was to determine the CCN resistance conferred by the Cre7 gene from Aegilops triuncialis in a 42-chromosome introgression line and to assess the effects of the Cre1, Cre3, Cre4, and Cre8 genes present in A...

Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

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Toraj KHABIRI

2013-02-01

Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

Development of a wheat-Aegilops searsii substitution line with positively affecting Chinese steamed bread quality.

Science.gov (United States)

Du, Xuye; Ma, Xin; Min, Jingzhi; Zhang, Xiaocun; Jia, Zhenzhen

2018-03-01

A wheat- Aegilops searsii substitution line GL1402, in which chromosome 1B was substituted with 1S s from Ae. searsii , was developed and detected using SDS-PAGE and GISH. The SDS-PAGE analysis showed that the HMW-GS encoded by the Glu-B1 loci of Chinese Spring was replaced by the HMW-GS encoded by the Glu-1S s loci of Ae. searsii . Glutenin macropolymer (GMP) investigation showed that GL1402 had a much higher GMP content than Chinese Spring did. A dough quality comparison of GL1402 and Chinese Spring indicated that GL1402 showed a significantly higher protein content and middle peak time (MPT), and a smaller right peak slope (RPS). Quality tests of Chinese steamed bread (CSB) showed that the GL1402 also produced good steamed bread quality. These results suggested that the substitution line is a valuable breeding material for improving the wheat processing quality.

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat

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Abdulqader Jighly

2018-02-01

Full Text Available Whole genome duplication (WGD is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome. The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy

Is Ancestor veneration the most universal of all world religions? A critique of modernist cosmological bias

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Thomas Reuter

2015-07-01

Full Text Available Research by anthropologists engaged with the Comparative Austronesia Project (Australian National University has amassed an enormous data set for ethnological comparison between the religions of Austronesian-speaking societies, a language group to which nearly all Indonesian societies also belong. Comparative analysis reveals that ancestor veneration is a key-shared feature among “Austronesian” religious cosmologies; a feature that also resonates strongly with the ancestor-focused religions characteristic of East Asia. Characteristically, the religions of Austronesian-speaking societies focus on the core idea of a sacred time and place of ancestral origin and the continuous flow of life that is issuing forth from this source. Present-day individuals connect with the place and time of origin though ritual acts of retracing a historical path of migration to its source. What can this seemingly exotic notion of a flow of life reveal about the human condition writ large? Is it merely a curiosity of the ethnographic record of this region, a traditional religious insight forgotten even by many of the people whose traditional religion this is, but who have come under the influence of so-called world religions? Or is there something of great importance to be learnt from the Austronesian approach to life? Such questions have remained unasked until now, I argue, because a systematic cosmological bias within western thought has largely prevented us from taking Ancestor Religion and other forms of “traditional knowledge” seriously as an alternative truth claim. While I have discussed elsewhere the significance of Ancestor Religion in reference to my own research in highland Bali, I will attempt in this paper to remove this bias by its roots. I do so by contrasting two modes of thought: the “incremental dualism” of precedence characteristic of Austronesian cultures and their Ancestor Religions, and the “transcendental dualism” of mind and

Dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon: comparison with common wheat and Aegilops peregrina.

Science.gov (United States)

Chen, Guanxing; Zhu, Jiantang; Zhou, Jianwen; Subburaj, Saminathan; Zhang, Ming; Han, Caixia; Hao, Pengchao; Li, Xiaohui; Yan, Yueming

2014-08-06

Thorough understanding of seed starch biosynthesis and accumulation mechanisms is of great importance for agriculture and crop improvement strategies. We conducted the first comprehensive study of the dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon and compared the findings with those reported for common wheat (Chinese Spring, CS) and Aegilops peregrina. Only B-granules were identified in Brachypodium Bd21, and the shape variation and development of starch granules were similar in the B-granules of CS and Bd21. Phylogenetic analysis showed that most of the Bd21 starch synthesis-related genes were more similar to those in wheat than in rice. Early expression of key genes in Bd21 starch biosynthesis mediate starch synthesis in the pericarp; intermediate-stage expression increases the number and size of starch granules. In contrast, these enzymes in CS and Ae. peregrina were mostly expressed at intermediate stages, driving production of new B-granules and increasing the granule size, respectively. Immunogold labeling showed that granule-bound starch synthase (GBSSI; related to amylose synthesis) was mainly present in starch granules: at lower levels in the B-granules of Bd21 than in CS. Furthermore, GBSSI was phosphorylated at threonine 183 and tyrosine 185 in the starch synthase catalytic domain in CS and Ae. peregrina, but neither site was phosphorylated in Bd21, suggesting GBSSI phosphorylation could improve amylose biosynthesis. Bd21 contains only B-granules, and the expression of key genes in the three studied genera is consistent with the dynamic development of starch granules. GBSSI is present in greater amounts in the B-granules of CS than in Bd21; two phosphorylation sites (Thr183 and Tyr185) were found in Triticum and Aegilops; these sites were not phosphorylated in Bd21. GBSSI phosphorylation may reflect its importance in amylose synthesis.

A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes

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Chad Jorgensen

2017-10-01

Full Text Available Wild emmer (Triticum turgidum ssp. dicoccoides is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. ‘Langdon’ x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum–Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.

Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species.

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Yoshihiro Matsuoka

Full Text Available The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome, namely Triticumturgidum L. (AABB genome and Aegilopstauschii Coss. (DD genome. An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL analysis showed that (1 production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2 first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3 six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated

Regions of the bread wheat D genome associated with variation in key photosynthesis traits and shoot biomass under both well watered and water deficient conditions.

Science.gov (United States)

Osipova, Svetlana; Permyakov, Alexey; Permyakova, Marina; Pshenichnikova, Tatyana; Verkhoturov, Vasiliy; Rudikovsky, Alexandr; Rudikovskaya, Elena; Shishparenok, Alexandr; Doroshkov, Alexey; Börner, Andreas

2016-05-01

A quantitative trait locus (QTL) approach was taken to reveal the genetic basis in wheat of traits associated with photosynthesis during a period of exposure to water deficit stress. The performance, with respect to shoot biomass, gas exchange and chlorophyll fluorescence, leaf pigment content and the activity of various ascorbate-glutathione cycle enzymes and catalase, of a set of 80 wheat lines, each containing a single chromosomal segment introgressed from the bread wheat D genome progenitor Aegilops tauschii, was monitored in plants exposed to various water regimes. Four of the seven D genome chromosomes (1D, 2D, 5D, and 7D) carried clusters of both major (LOD >3.0) and minor (LOD between 2.0 and 3.0) QTL. A major QTL underlying the activity of glutathione reductase was located on chromosome 2D, and another, controlling the activity of ascorbate peroxidase, on chromosome 7D. A region of chromosome 2D defined by the microsatellite locus Xgwm539 and a second on chromosome 7D flanked by the marker loci Xgwm1242 and Xgwm44 harbored a number of QTL associated with the water deficit stress response.

The Waikato river: Changing properties of a living Māori ancestor

NARCIS (Netherlands)

Meijl, A.H.M. van

2015-01-01

In Māori cosmology, rivers and other waterways are conceptualised as living ancestors, who have their own life force and spiritual strength. The special status of rivers in Māori society also explains why they are sometimes separated from other Māori claims to natural resources of which they were

Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)

Czech Academy of Sciences Publication Activity Database

Akpinar, B. A.; Lucas, S. J.; Vrána, Jan; Doležel, Jaroslav; Budak, H.

2015-01-01

Roč. 13, č. 6 (2015), s. 740-752 ISSN 1467-7644 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : D genome donor of wheat * chromosome 5D * comparative genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.090, year: 2015

Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.

Science.gov (United States)

Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

2014-09-01

Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny.

Evolution of life history and behavior in Hominidae: towards phylogenetic reconstruction of the chimpanzee-human last common ancestor.

Science.gov (United States)

Duda, Pavel; Zrzavý, Jan

2013-10-01

The origin of the fundamental behavioral differences between humans and our closest living relatives is one of the central issues of evolutionary anthropology. The prominent, chimpanzee-based referential model of early hominin behavior has recently been challenged on the basis of broad multispecies comparisons and newly discovered fossil evidence. Here, we argue that while behavioral data on extant great apes are extremely relevant for reconstruction of ancestral behaviors, these behaviors should be reconstructed trait by trait using formal phylogenetic methods. Using the widely accepted hominoid phylogenetic tree, we perform a series of character optimization analyses using 65 selected life-history and behavioral characters for all extant hominid species. This analysis allows us to reconstruct the character states of the last common ancestors of Hominoidea, Hominidae, and the chimpanzee-human last common ancestor. Our analyses demonstrate that many fundamental behavioral and life-history attributes of hominids (including humans) are evidently ancient and likely inherited from the common ancestor of all hominids. However, numerous behaviors present in extant great apes represent their own terminal autapomorphies (both uniquely derived and homoplastic). Any evolutionary model that uses a single extant species to explain behavioral evolution of early hominins is therefore of limited use. In contrast, phylogenetic reconstruction of ancestral states is able to provide a detailed suite of behavioral, ecological and life-history characters for each hypothetical ancestor. The living great apes therefore play an important role for the confident identification of the traits found in the chimpanzee-human last common ancestor, some of which are likely to represent behaviors of the fossil hominins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Windmills: Ancestors of the wind power generation

Institute of Scientific and Technical Information of China (English)

Cesare ROSSI; Flavio RUSSO; Sergio SAVINO

2017-01-01

A brief description of the windmills from the second millennium BC to the Renaissance is presented.This survey is a part of several studies conducted by the authors on technology in the ancient world.The windmills are the first motor,other than human muscles,and are the ancestors of the modem wind turbines.Some authors' virtual reconstructions of old windmills are also presented.The paper shows that the operating principle of many modem machines had already been conceived in the ancient times by using a technology that was more advanced than expected,but with two main differences,as follows:Similar tasks were accomplished by using much less energy;and the environmental impact was nil or very low.Modem designers should sometimes consider simplicity rather than the use of a large amount of energy.

Windmills: Ancestors of the wind power generation

Science.gov (United States)

Rossi, Cesare; Russo, Flavio; Savino, Sergio

2017-09-01

A brief description of the windmills from the second millennium BC to the Renaissance is presented. This survey is a part of several studies conducted by the authors on technology in the ancient world. The windmills are the first motor, other than human muscles, and are the ancestors of the modern wind turbines. Some authors' virtual reconstructions of old windmills are also presented. The paper shows that the operating principle of many modern machines had already been conceived in the ancient times by using a technology that was more advanced than expected, but with two main differences, as follows: Similar tasks were accomplished by using much less energy; and the environmental impact was nil or very low. Modern designers should sometimes consider simplicity rather than the use of a large amount of energy.

Expression pattern of salt tolerance-related genes in Aegilops cylindrica.

Science.gov (United States)

Arabbeigi, Mahbube; Arzani, Ahmad; Majidi, Mohammad Mahdi; Sayed-Tabatabaei, Badraldin Ebrahim; Saha, Prasenjit

2018-02-01

Aegilops cylindrica , a salt-tolerant gene pool of wheat, is a useful plant model for understanding mechanism of salt tolerance. A salt-tolerant USL26 and a salt-sensitive K44 genotypes of A. cylindrica , originating from Uremia Salt Lake shores in Northwest Iran and a non-saline Kurdestan province in West Iran, respectively, were identified based on screening evaluation and used for this work. The objective of the current study was to investigate the expression patterns of four genes related to ion homeostasis in this species. Under treatment of 400 mM NaCl, USL26 showed significantly higher root and shoot dry matter levels and K + concentrations, together with lower Na + concentrations than K44 genotype. A. cylindrica HKT1;5 ( AecHKT1;5 ), SOS1 ( AecSOS1 ), NHX1 ( AecNHX1 ) and VP1 ( AecVP1 ) were partially sequenced to design each gene specific primer. Quantitative real-time PCR showed a differential expression pattern of these genes between the two genotypes and between the root and shoot tissues. Expressions of AecHKT1;5 and AecSOS1 was greater in the roots than in the shoots of USL26 while AecNHX1 and AecVP1 were equally expressed in both tissues of USL26 and K44. The higher transcripts of AecHKT1;5 in the roots versus the shoots could explain both the lower Na + in the shoots and the much lower Na + and higher K + concentrations in the roots/shoots of USL26 compared to K44. Therefore, the involvement of AecHKT1;5 in shoot-to-root handover of Na + in possible combination with the exclusion of excessive Na + from the root in the salt-tolerant genotype are suggested.

Correction to: A sophisticated, differentiated Golgi in the ancestor of eukaryotes.

Science.gov (United States)

Barlow, Lael D; Nývltová, Eva; Aguilar, Maria; Tachezy, Jan; Dacks, Joel B

2018-03-28

Upon publication of the original article, Barlow et al. [1], the authors noticed that Fig. 4b contained an inaccuracy when additional data is taken into account. We inferred a loss of GRASP in the common ancestor of cryptophytes and archaeplastids, based on the absence of identified homologues in the data from taxa that we analyzed, which include Cyanidioschyzon merolae as the single representative of red algae.

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

KAUST Repository

Refregier, Guislaine

2016-10-14

Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term = 0.03 SNP/genome/year, derived from a tuberculosis ancestor of around 70,000 years old; intermediate = 0.2 SNP/genome/year derived from a Peruvian mummy; short-term = 0.5 SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as “T3-Osa-Tur”) shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800 y and 2000 years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor.

Science.gov (United States)

Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe

2016-11-01

Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional

Heterokont predator Develorapax marinus gen. et sp. nov. – a model of the ochrophyte ancestor

Directory of Open Access Journals (Sweden)

Vladimir V. Aleoshin

2016-08-01

Full Text Available Heterotrophic lineages of Heterokonta (or stramenopiles, in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heteretrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor. Here we present a new genus and species of marine free-living heterotrophic heterokont Develorapax marinus, which falls into an isolated heterokont cluster, along with the marine flagellate Developayella elegans, and is able to engulf eukaryotic cells. Together with environmental sequences D. marinus and D. elegans form a class-level clade Developea nom. nov. represented by species adapted to different environmental conditions and with a wide geographical distribution. The position of Developea among Heterokonta in large-scale phylogenetic tree is discussed. We propose that members of the Developea clade represent a model for transition from bacterivory to a predatory feeding mode by selection for larger prey. Presumably, such transition in the grazing strategy is possible in the presence of bacterial biofilms, and has likely occured in the ochrophyte ancestor.

Wheat multiple synthetic derivatives: a new source for heat stress tolerance adaptive traits

Science.gov (United States)

Elbashir, Awad Ahmed Elawad; Gorafi, Yasir Serag Alnor; Tahir, Izzat Sidahmed Ali; Kim, June-Sik; Tsujimoto, Hisashi

2017-01-01

Heat stress is detrimental to wheat (Triticum aestivum L.) productivity. In this study, we aimed to select heat-tolerant plants from a multiple synthetic derivatives (MSD) population and evaluate their agronomic and physiological traits. We selected six tolerant plants from the population with the background of the cultivar ‘Norin 61’ (N61) and established six MNH (MSD population of N61 selected as heat stress-tolerant) lines. We grew these lines with N61 in the field and growth chamber. In the field, we used optimum and late sowings to ensure plant exposure to heat. In the growth chamber, in addition to N61, we used the heat-tolerant cultivars ‘Gelenson’ and ‘Bacanora’. We confirmed that MNH2 and MNH5 lines acquired heat tolerance. These lines had higher photosynthesis and stomata conductance and exhibited no reduction in grain yield and biomass under heat stress compared to N61. We noticed that N61 had relatively good adaptability to heat stress. Our results indicate that the MSD population includes the diversity of Aegilops tauschii and is a promising resource to uncover useful quantitative traits derived from this wild species. Selected lines could be useful for heat stress tolerance breeding. PMID:28744178

Healing and coping with life within challenges of spiritual insecurity: Juxtaposed consideration of Christ’s sinlessness and African ancestors in pastoral guidance

Directory of Open Access Journals (Sweden)

Vhumani Magezi

2017-04-01

Full Text Available Spiritual insecurity among African Christians is a huge challenge. The insecurity among other things arises from African people’s former traditional African ancestral world view of ancestral veneration. The ancestors promote or hinder African Christians’ reliance on Christ because they have presupposedly acquired the supernatural power that enables them to provide diagnoses and solutions to life challenges. The inherent problem in the ancestral world view, however, is that the ancestors are both respected and feared by their descendants because they can either bless or harm depending on the state of the relationship between the surviving human beings and the ancestors. The basis of the unpredictable influence of ancestors lies in the fact that they (ancestors are considered as human beings who carry their human qualities to the spiritual world. In light of this situation, one constructive approach that can be advanced to address the challenges of African Christians’ spiritual insecurity is a proper understanding of Christ as a sinless representative of humanity. This approach maintains that healing and coping with life within the challenge of African spirituality in the context of threatening life issues can be addressed by an appropriate understanding of Christ’s sinlessness. The article argues for the foundational status of Christ as a sinless representative of humanity as the controlling framework. In doing so, Christ’s sinlessness and the sinfulness of natural ancestors are juxtaposed to compare the two ontologies in order to draw some pastoral guidelines for African Christians. This approach pays close attention to the factors and mindset that sustain people who adhere to ancestral worship and assess them through a lens of Christology focusing on Christ’s sinlessness as an exemplary doctrine.

Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis Eig) into bread wheat (Triticum aestivum L.).

Science.gov (United States)

Millet, E; Manisterski, J; Ben-Yehuda, P; Distelfeld, A; Deek, J; Wan, A; Chen, X; Steffenson, B J

2014-06-01

Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cultivar Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.

Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution.

Science.gov (United States)

Wang, X; Zhao, L; Zhang, L; Wu, Y; Chou, M; Wei, G

2018-07-01

Rhizobial symbiotic plasmids play vital roles in mutualistic symbiosis with legume plants by executing the functions of nodulation and nitrogen fixation. To explore the gene composition and genetic constitution of rhizobial symbiotic plasmids, comparison analyses of 24 rhizobial symbiotic plasmids derived from four rhizobial genera was carried out. Results illustrated that rhizobial symbiotic plasmids had higher proportion of functional genes participating in amino acid transport and metabolism, replication; recombination and repair; carbohydrate transport and metabolism; energy production and conversion and transcription. Mesorhizobium amorphae CCNWGS0123 symbiotic plasmid - pM0123d had similar gene composition with pR899b and pSNGR234a. All symbiotic plasmids shared 13 orthologous genes, including five nod and eight nif/fix genes which participate in the rhizobia-legume symbiosis process. These plasmids contained nod genes from four ancestors and fix genes from six ancestors. The ancestral type of pM0123d nod genes was similar with that of Rhizobium etli plasmids, while the ancestral type of pM0123d fix genes was same as that of pM7653Rb. The phylogenetic trees constructed based on nodCIJ and fixABC displayed different topological structures mainly due to nodCIJ and fixABC ancestral type discordance. The study presents valuable insights into mosaic structures and the evolution of rhizobial symbiotic plasmids. This study compared 24 rhizobial symbiotic plasmids that included four genera and 11 species, illuminating the functional gene composition and symbiosis gene ancestor types of symbiotic plasmids from higher taxonomy. It provides valuable insights into mosaic structures and the evolution of symbiotic plasmids. © 2018 The Society for Applied Microbiology.

Before the dawn recovering the lost history of our ancestors

CERN Document Server

Wade, Nicholas

2007-01-01

Nicholas Wade’s articles are a major reason why the science section has become the most popular, nationwide, in the New York Times. In his groundbreaking Before the Dawn, Wade reveals humanity’s origins as never before—a journey made possible only recently by genetic science, whose incredible findings have answered such questions as: What was the first human language like? How large were the first societies, and how warlike were they? When did our ancestors first leave Africa, and by what route did they leave? By eloquently solving these and numerous other mysteries, Wade offers nothing less than a uniquely complete retelling of a story that began 500 centuries ago.

Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor.

Science.gov (United States)

Redmond, Anthony K; Pettinello, Rita; Dooley, Helen

2017-03-01

The molecular machinery required for lymphocyte development and differentiation appears to have emerged concomitantly with distinct B- and T-like lymphocyte subsets in the ancestor of all vertebrates. The TNFSF superfamily (TNFSF) members BAFF (TNFSF13/Blys) and APRIL (TNFSF13) are key regulators of B cell development survival, and activation in mammals, but the temporal emergence of these molecules, and their precise relationship to the newly identified TNFSF gene BALM (BAFF and APRIL-like molecule), have not yet been elucidated. Here, to resolve the early evolutionary history of this family, we improved outgroup sampling and alignment quality, and applied better fitting substitution models compared to past studies. Our analyses reveal that BALM is a definitive TNFSF13 family member, which split from BAFF in the gnathostome (jawed vertebrate) ancestor. Most importantly, however, we show that both the APRIL and BAFF lineages existed in the ancestors of all extant vertebrates. This implies that APRIL has been lost, or is yet to be found, in cyclostomes (jawless vertebrates). Our results suggest that lineage-specific gene duplication and loss events have caused lymphocyte regulation, despite shared origins, to become secondarily distinct between gnathostomes and cyclostomes. Finally, the structure of lamprey BAFF-like, and its phylogenetic placement as sister to BAFF and BALM, but not the more slowly evolving APRIL, indicates that the primordial lymphocyte regulator was more APRIL-like than BAFF-like.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

OpenAIRE

Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes...

“Ancestors We Didn’t Even Know We Had”: Alice Walker, Asian Religion, and Ethnic Authenticity

Directory of Open Access Journals (Sweden)

Kyle Garton-Gundling

2015-03-01

Full Text Available Recent debates about the ethics of identity in a global age have dealt with how to prioritize conflicting local and global allegiances. Guided by these concerns, the fiction of Alice Walker develops a distinctive view of how local cultures and global movements can fruitfully interact. This vision depends on concepts from Asian religions, a major influence that critics of Walker have largely overlooked. Walker promotes Hindu and Buddhist meditation in a context of widespread African American skepticism toward Asian religions. According to widespread notions of cultural authenticity, Asian religions cannot nourish an African American connection to ethnic roots. In response to this challenge, Alice Walker’s fiction portrays Hindu and Buddhist mystics as African Americans’ ancestors, thus positioning these faiths as authentically black. By creatively enfolding Asian religions into her sense of African American heritage, Walker builds a spiritual cosmopolitanism that relies on claims of ancestral affiliation even when these claims are not literal. This strategy is Walker’s effort to create a new paradigm of cultural authenticity, one that allows individuals and groups to choose their ancestors. Walker’s approach seeks to incorporate disparate global influences while still valorizing the figure of the ancestor. This innovative approach places Walker at the forefront of a growing number of African American artists and intellectuals who promote Asian religions to American minorities. Walker’s work vividly dramatizes larger concerns in transnational American Studies: Eastern philosophy’s relevance to identity politics, the tensions between universal ideals and cultural specifics, and the ethics of cross-cultural appropriation.

Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene.

Science.gov (United States)

Guo, Zhiai; Song, Yanxia; Zhou, Ronghua; Ren, Zhenglong; Jia, Jizeng

2010-02-01

Ppd-D1 is one of the most potent genes affecting the photoperiod response of wheat (Triticum aestivum). Only two alleles, insensitive Ppd-D1a and sensitive Ppd-D1b, were known previously, and these did not adequately explain the broad adaptation of wheat to photoperiod variation. In this study, five diagnostic molecular markers were employed to identify Ppd-D1 haplotypes in 492 wheat varieties from diverse geographic locations and 55 accessions of Aegilops tauschii, the D genome donor species of wheat. Six Ppd-D1 haplotypes, designated I-VI, were identified. Types II, V and VI were considered to be more ancient and types I, III and IV were considered to be derived from type II. The transcript abundances of the Ppd-D1 haplotypes showed continuous variation, being highest for haplotype I, lowest for haplotype III, and correlating negatively with varietal differences in heading time. These haplotypes also significantly affected other agronomic traits. The distribution frequency of Ppd-D1 haplotypes showed partial correlations with both latitudes and altitudes of wheat cultivation regions. The evolution, expression and distribution of Ppd-D1 haplotypes were consistent evidentially with each other. What was regarded as a pair of alleles in the past can now be considered a series of alleles leading to continuous variation.

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

Directory of Open Access Journals (Sweden)

Shairul Izan

2017-08-01

Full Text Available Whole Genome Shotgun (WGS sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb, Aegilops tauschii (4 Gb and Paphiopedilum henryanum (25 Gb. We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.

Cloning and characterization of novel γ-gliadin genes from Aegilops markgrafii in relation to evolution and wheat breeding

Directory of Open Access Journals (Sweden)

Min Li

2017-08-01

Full Text Available Gliadins are the major components of storage proteins in wheat and play an important role in determining the extensibility properties of dough. In the present work, six novel full-length γ-gliadin genes were cloned from the C genome of Aegilops markgrafii using a PCR-based strategy. Analysis of the deduced amino acid sequences showed that the cloned genes had primary structures that were similar, but not identical, to published γ-gliadins from other wheat-related species. The lengths of the open reading frames (ORFs ranged from 909 to 963 bp, and the repetitive and glutamine-rich domains were mainly responsible for the size of the proteins. An extra cysteine residue was present in the repetitive domain of sequence JX566513. All amino acid sequences of γ-gliadin genes from Ae. markgrafii were searched for the five peptides identified as T cell stimulatory epitopes in celiac disease (CD patients. Peptide Gliγ-3 was present in sequences JX566513 and JX566514. Peptide Gliγ-5 was present only in JX566513. The other γ-gliadins contained no toxic epitopes. These results provide information to better understand the use of Ae. markgrafii in wheat breeding and the evolutionary relationship of the γ-gliadin genes in Ae. markgrafii and other Triticeae species.

Extensive intron gain in the ancestor of placental mammals

Science.gov (United States)

2011-01-01

Background Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures. Results A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals. Conclusions This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The

Ontogeny of the maxilla in Neanderthals and their ancestors.

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Lacruz, Rodrigo S; Bromage, Timothy G; O'Higgins, Paul; Arsuaga, Juan-Luis; Stringer, Chris; Godinho, Ricardo Miguel; Warshaw, Johanna; Martínez, Ignacio; Gracia-Tellez, Ana; de Castro, José María Bermúdez; Carbonell, Eudald

2015-12-07

Neanderthals had large and projecting (prognathic) faces similar to those of their putative ancestors from Sima de los Huesos (SH) and different from the retracted modern human face. When such differences arose during development and the morphogenetic modifications involved are unknown. We show that maxillary growth remodelling (bone formation and resorption) of the Devil's Tower (Gibraltar 2) and La Quina 18 Neanderthals and four SH hominins, all sub-adults, show extensive bone deposition, whereas in modern humans extensive osteoclastic bone resorption is found in the same regions. This morphogenetic difference is evident by ∼5 years of age. Modern human faces are distinct from those of the Neanderthal and SH fossils in part because their postnatal growth processes differ markedly. The growth remodelling identified in these fossil hominins is shared with Australopithecus and early Homo but not with modern humans suggesting that the modern human face is developmentally derived.

Within- and trans-generational plasticity affects the opportunity for selection in barbed goatgrass (Aegilops triuncialis).

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Espeland, Erin K; Rice, Kevin J

2012-12-01

Environments are composed of selective agents, and environments may also modify the efficacy of these agents. Environments affect the rate of maximum evolutionary change by influencing variation in relative fitness (i.e., the opportunity for selection, or I). Within- and transgenerational plastic environmental responses may affect I, speeding or slowing processes of local adaptation. • We determined whether environmental factors affected the opportunity for selection (I) in Aegilops triuncialis (barbed goatgrass) by measuring I as a within- and transgenerational plastic response to two maternal glasshouse environments (serpentine/dry and loam/moist). We also determined whether this species' two most common genetic lineages (determined by DNA microsatellite length polymorphism) varied in response to glasshouse treatments. • Opportunity for selection was less for plants grown in the dry serpentine environment than for plants grown in the moist loam environment. This response varied between genetic lineages. The east lineage exhibited a within-generation response to the dry serpentine environment. For both seed mass and average seed weight in this lineage, the opportunity for selection was lower in dry serpentine than in moist loam. The west lineage had a transgenerational response to the dry serpentine such that the opportunity for selection for seed number and seed mass was lower for plants produced by mothers grown in dry serpentine than for plants produced by mothers in moist loam. • Phenotypic variation in relative fitness is constrained by the dry serpentine environment, which leads to lower evolvability in this environment. Within- and transgenerational effects of the environment may slow local adaptation to serpentine soils.

A proposal of the proteome before the last universal common ancestor (LUCA)

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de Farias, Sávio Torres; Rêgo, Thais Gaudêncio; José, Marco V.

2016-01-01

The search for understanding the biological nature of the last universal common ancestor (LUCA) has been a theoretical challenge and has sparked intense debate in the scientific community. We reconstructed the ancestral sequences of tRNAs in order to test the hypothesis that these molecules originated the first genes. The results showed that the proteome before LUCA may have been composed of basal energy metabolism, namely, compounds with three carbons in the glycolytic pathway, which operated as a distribution centre of substrates for the development of metabolic pathways of nucleotides, lipids and amino acids. Thus, we present a proposal for metabolism in organisms before LUCA that was the initial core for the assembly of further metabolic pathways.

ThMYC4E, candidate Blue aleurone 1 gene controlling the associated trait in Triticum aestivum.

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Na Li

Full Text Available Blue aleurone is a useful and interesting trait in common wheat that was derived from related species. Here, transcriptomes of blue and white aleurone were compared for isolating Blue aleurone 1 (Ba1 transferred from Thinopyrum ponticum. In the genes involved in anthocyanin biosynthesis, only a basic helix-loop-helix (bHLH transcription factor, ThMYC4E, had a higher transcript level in blue aleurone phenotype, and was homologous to the genes on chromosome 4 of Triticum aestivum. ThMYC4E carried the characteristic domains (bHLH-MYC_N, HLH and ACT-like of a bHLH transcription factor, and clustered with genes regulating anthocyanin biosynthesis upon phylogenetic analysis. The over-expression of ThMYC4E regulated anthocyanin biosynthesis with the coexpression of the MYB transcription factor ZmC1 from maize. ThMYC4E existed in the genomes of the addition, substitution and near isogenic lines with the blue aleurone trait derived from Th. ponticum, and could not be detected in any germplasm of T. urartu, T. monococcum, T. turgidum, Aegilops tauschii or T. aestivum, with white aleurone. These results suggested that ThMYC4E was candidate Ba1 gene controlling the blue aleurone trait in T. aestivum genotypes carrying Th. ponticum introgression. The ThMYC4E isolation aids in better understanding the genetic mechanisms of the blue aleurone trait and in its more effective use during wheat breeding.

PARTIAL REPRODUCTIVE ISOLATION OF A RECENTLY DERIVED RESIDENT-FRESHWATER POPULATION OF THREESPINE STICKLEBACK (GASTEROSTEUS ACULEATUS) FROM ITS PUTATIVE ANADROMOUS ANCESTOR

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Furin, Christoff G.; Von Hippel, Frank A.; Bell, Michael A.

2012-01-01

We used no-choice mating trials to test for assortative mating between a newly derived resident-freshwater population (8 – 22 generations since founding) of threespine stickleback (Gasterosteus aculeatus) in Loberg Lake, Alaska and its putative anadromous ancestor as well as a morphologically convergent but distantly related resident-freshwater population. Partial reproductive isolation has evolved between the Loberg Lake population and its ancestor within a remarkably short time period. However, Loberg stickleback readily mate with morphologically similar, but distantly related resident-freshwater stickleback. Partial pre-mating isolation is asymmetrical; anadromous females and smaller, resident-freshwater males from Loberg Lake readily mate, but the anadromous males and smaller Loberg females do not. Our results indicate that pre-mating isolation can begin to evolve in allopatry within a few generations after isolation as a correlated effect of evolution of reduced body size. PMID:23025615

Chemical interactions between plants in Mediterranean vegetation: the influence of selected plant extracts on Aegilops geniculata metabolome.

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Scognamiglio, Monica; Fiumano, Vittorio; D'Abrosca, Brigida; Esposito, Assunta; Choi, Young Hae; Verpoorte, Robert; Fiorentino, Antonio

2014-10-01

Allelopathy is the chemical mediated communication among plants. While on one hand there is growing interest in the field, on the other hand it is still debated as doubts exist at different levels. A number of compounds have been reported for their ability to influence plant growth, but the existence of this phenomenon in the field has rarely been demonstrated. Furthermore, only few studies have reported the uptake and the effects at molecular level of the allelochemicals. Allelopathy has been reported on some plants of Mediterranean vegetation and could contribute to structuring this ecosystem. Sixteen plants of Mediterranean vegetation have been selected and studied by an NMR-based metabolomics approach. The extracts of these donor plants have been characterized in terms of chemical composition and the effects on a selected receiving plant, Aegilops geniculata, have been studied both at the morphological and at the metabolic level. Most of the plant extracts employed in this study were found to have an activity, which could be correlated with the presence of flavonoids and hydroxycinnamate derivatives. These plant extracts affected the receiving plant in different ways, with different rates of growth inhibition at morphological level. The results of metabolomic analysis of treated plants suggested the induction of oxidative stress in all the receiving plants treated with active donor plant extracts, although differences were observed among the responses. Finally, the uptake and transport into receiving plant leaves of different metabolites present in the extracts added to the culture medium were observed. Copyright © 2014 Elsevier Ltd. All rights reserved.

iTRAQ-Based Proteomics Analyses of Sterile/Fertile Anthers from a Thermo-Sensitive Cytoplasmic Male-Sterile Wheat with Aegilops kotschyi Cytoplasm

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Gaoming Zhang

2018-05-01

Full Text Available A “two-line hybrid system” was developed, previously based on thermo-sensitive cytoplasmic male sterility in Aegilops kotschyi (K-TCMS, which can be used in wheat breeding. The K-TCMS line exhibits complete male sterility and it can be used to produce hybrid wheat seeds during the normal wheat-growing season; it propagates via self-pollination at high temperatures. Isobaric tags for relative and absolute quantification-based quantitative proteome and bioinformatics analyses of the TCMS line KTM3315A were conducted under different fertility conditions to understand the mechanisms of fertility conversion in the pollen development stages. In total, 4639 proteins were identified, the differentially abundant proteins that increased/decreased in plants with differences in fertility were mainly involved with energy metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, protein synthesis, translation, folding, and degradation. Compared with the sterile condition, many of the proteins that related to energy and phenylpropanoid metabolism increased during the anther development stage. Thus, we suggest that energy and phenylpropanoid metabolism pathways are important for fertility conversion in K-TCMS wheat. These findings provide valuable insights into the proteins involved with anther and pollen development, thereby, helping to further understand the mechanism of TCMS in wheat.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life.

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Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-12-19

The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral ("high ancestrality"). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes.

The origin of life and the last universal common ancestor: do we need a change of perspective?

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Glansdorff, Nicolas; Xu, Ying; Labedan, Bernard

2009-09-01

A complete tree with roots, trunk and crown remains an appropriate model to represent all steps of life's development, from the emergence of a unique genetic code up to the last universal common ancestor and its further radiation. Catalytic closure of a mixture of prebiotic polymers is a heuristic alternative to the RNA world. Conjectures about emergence of life in an infinite multiverse should not confuse probability with possibility.

Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants.

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Hetherington, Alexander J; Dolan, Liam

2018-02-05

There are two general types of rooting systems in extant land plants: gametophyte rhizoids and sporophyte root axes. These structures carry out the rooting function in the free-living stage of almost all land plant gametophytes and sporophytes, respectively. Extant vascular plants develop a dominant, free-living sporophyte on which roots form, with the exception of a small number of taxa that have secondarily lost roots. However, fossil evidence indicates that early vascular plants did not develop sporophyte roots. We propose that the common ancestor of vascular plants developed a unique rooting system-rhizoidal sporophyte axes. Here we present a synthesis and reinterpretation of the rootless sporophytes of Horneophyton lignieri , Aglaophyton majus , Rhynia gwynne-vaughanii and Nothia aphylla preserved in the Rhynie chert. We show that the sporophyte rooting structures of all four plants comprised regions of plagiotropic (horizontal) axes that developed unicellular rhizoids on their underside. These regions of axes with rhizoids developed bilateral symmetry making them distinct from the other regions which were radially symmetrical. We hypothesize that rhizoidal sporophyte axes constituted the rooting structures in the common ancestor of vascular plants because the phylogenetic positions of these plants span the origin of the vascular lineage.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'. © 2017 The Authors.

Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum lines

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Qi Bao

2012-01-01

Full Text Available Abstract Background Alteration in gene expression resulting from allopolyploidization is a prominent feature in plants, but its spectrum and extent are not fully known. Common wheat (Triticum aestivum was formed via allohexaploidization about 10,000 years ago, and became the most important crop plant. To gain further insights into the genome-wide transcriptional dynamics associated with the onset of common wheat formation, we conducted microarray-based genome-wide gene expression analysis on two newly synthesized allohexaploid wheat lines with chromosomal stability and a genome constitution analogous to that of the present-day common wheat. Results Multi-color GISH (genomic in situ hybridization was used to identify individual plants from two nascent allohexaploid wheat lines between Triticum turgidum (2n = 4x = 28; genome BBAA and Aegilops tauschii (2n = 2x = 14; genome DD, which had a stable chromosomal constitution analogous to that of common wheat (2n = 6x = 42; genome BBAADD. Genome-wide analysis of gene expression was performed for these allohexaploid lines along with their parental plants from T. turgidum and Ae. tauschii, using the Affymetrix Gene Chip Wheat Genome-Array. Comparison with the parental plants coupled with inclusion of empirical mid-parent values (MPVs revealed that whereas the great majority of genes showed the expected parental additivity, two major patterns of alteration in gene expression in the allohexaploid lines were identified: parental dominance expression and non-additive expression. Genes involved in each of the two altered expression patterns could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Strikingly, whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes was highly stochastic, consistent with the involvement of diverse Gene Ontology (GO

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

Science.gov (United States)

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. Conclusion While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral (“high ancestrality”). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes. Reviewers This article was reviewed by Martijn A Huynen, Toni Gabaldón and Fyodor Kondrashov. PMID:24354654

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Czech Academy of Sciences Publication Activity Database

Luo, M.C.; Gu, Y.Q.; You, F.M.; Deal, K.R.; Šimková, Hana; Doležel, Jaroslav; Anderson, O.D.; Dvorak, J.

2013-01-01

Roč. 110, č. 19 (2013), s. 7940-7945 ISSN 0027-8424 R&D Projects: GA ČR(CZ) GAP501/12/2554 Institutional research plan: CEZ:AV0Z50380511 Keywords : single nucleotide polymorphism * synteny * gene density Subject RIV: EB - Genetic s ; Molecular Biology Impact factor: 9.809, year: 2013

Algal ancestor of land plants was preadapted for symbiosis.

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Delaux, Pierre-Marc; Radhakrishnan, Guru V; Jayaraman, Dhileepkumar; Cheema, Jitender; Malbreil, Mathilde; Volkening, Jeremy D; Sekimoto, Hiroyuki; Nishiyama, Tomoaki; Melkonian, Michael; Pokorny, Lisa; Rothfels, Carl J; Sederoff, Heike Winter; Stevenson, Dennis W; Surek, Barbara; Zhang, Yong; Sussman, Michael R; Dunand, Christophe; Morris, Richard J; Roux, Christophe; Wong, Gane Ka-Shu; Oldroyd, Giles E D; Ané, Jean-Michel

2015-10-27

Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis.

Impact of transgene genome location on gene migration from herbicide-resistant wheat (Triticum aestivum L.) to jointed goatgrass (Aegilops cylindrica Host).

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Rehman, Maqsood; Hansen, Jennifer L; Mallory-Smith, Carol A; Zemetra, Robert S

2017-08-01

Wheat (Triticum aestivum) (ABD) and jointed goatgrass (Aegilops cylindrica) (CD) can cross and produce hybrids that can backcross to either parent. Such backcrosses can result in progeny with chromosomes and/or chromosome segments retained from wheat. Thus, a herbicide resistance gene could migrate from wheat to jointed goatgrass. In theory, the risk of gene migration from herbicide-resistant wheat to jointed goatgrass is more likely if the gene is located on the D genome and less likely if the gene is located on the A or B genome of wheat. BC 1 populations (jointed goatgrass as a recurrent parent) were analyzed for chromosome numbers and transgene transmission rates under sprayed and non-sprayed conditions. Transgene retention in the non-sprayed BC 1 generation for the A, B and D genomes was 84, 60 and 64% respectively. In the sprayed populations, the retention was 81, 59 and 74% respectively. The gene transmission rates were higher than the expected 50% or less under sprayed and non-sprayed conditions, possibly owing to meiotic chromosome restitution and/or chromosome non-disjunction. Such high transmission rates in the BC 1 generation negates the benefits of gene placement for reducing the potential of gene migration from wheat to jointed goatgrass. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Ancestor-descendant relationships in evolution: origin of the extant pygmy right whale, Caperea marginata.

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Tsai, Cheng-Hsiu; Fordyce, R Ewan

2015-01-01

Ancestor-descendant relationships (ADRs), involving descent with modification, are the fundamental concept in evolution, but are usually difficult to recognize. We examined the cladistic relationship between the only reported fossil pygmy right whale, †Miocaperea pulchra, and its sole living relative, the enigmatic pygmy right whale Caperea marginata, the latter represented by both adult and juvenile specimens. †Miocaperea is phylogenetically bracketed between juvenile and adult Caperea marginata in morphologically based analyses, thus suggesting a possible ADR-the first so far identified within baleen whales (Cetacea: Mysticeti). The †Miocaperea-Caperea lineage may show long-term morphological stasis and, in turn, punctuated equilibrium. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s).

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Niranjana, M; Vinod; Sharma, J B; Mallick, Niharika; Tomar, S M S; Jha, S K

2017-12-01

Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F 1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

In pursuit of our ancestors' hand laterality.

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Bargalló, Amèlia; Mosquera, Marina; Lozano, Sergi

2017-10-01

The aim of this paper is to apply a previously published method (Bargalló and Mosquera, 2014) to the archaeological record, allowing us to identify the hand laterality of our ancestors and determine when and how this feature, which is exhibited most strongly in humans, appeared in our evolutionary history. The method focuses on identifying handedness by looking at the technical features of the flakes produced by a single knapper, and discovering how many flakes are required to ascertain their hand preference. This method can potentially be applied to the majority of archaeological sites, since flakes are the most abundant stone tools, and stone tools are the most widespread and widely-preserved remains from prehistory. For our study, we selected two Spanish sites: Gran Dolina-TD10.1 (Atapuerca) and Abric Romaní (Barcelona), which were occupied by pre-Neanderthal and Neanderthal populations, respectively. Our analyses indicate that a minimum number of eight flakes produced by the same knapper is required to ascertain their hand preference. Even though this figure is relatively low, it is quite difficult to obtain from many archaeological sites. In addition, there is no single technical feature that provides information about handedness, instead there is a combination of eight technical features, localised on the striking platforms and ventral surfaces. The raw material is not relevant where good quality rocks are used, in this case quartzite and flint, since most of them retain the technical features required for the analysis. Expertise is not an issue either, since the technical features analysed here only correlate with handedness (Bargalló and Mosquera, 2014). Our results allow us to tentatively identify one right-handed knapper among the pre-Neanderthals of level TD10.1 at Gran Dolina (Atapuerca), while four of the five Neanderthals analysed from Abric Romaní were right-handed. The hand preference of the fifth knapper from that location (AR5) remains unclear

Generation of amphidiploids from hybrids of wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum as a source of genetic variation for wheat improvement.

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Nemeth, Csilla; Yang, Cai-yun; Kasprzak, Paul; Hubbart, Stella; Scholefield, Duncan; Mehra, Surbhi; Skipper, Emma; King, Ian; King, Julie

2015-02-01

We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of F1 hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat-related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits.

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.

KAUST Repository

Wang, Jianli; Lee, Alison P; Kodzius, Rimantas; Brenner, Sydney; Venkatesh, Byrappa

2009-01-01

Stephen (2008) identified 13,736 ultraconserved elements (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes. In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes. These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.

KAUST Repository

Wang, Jianli

2009-03-01

Stephen (2008) identified 13,736 ultraconserved elements (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes. In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes. These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

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Cantine, Marjorie D.; Fournier, Gregory P.

2018-03-01

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life's persistence on a changing planet.

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

Directory of Open Access Journals (Sweden)

Manuel Michaël

2010-02-01

Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

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Natalia Borowska-Zuchowska

2016-10-01

Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner

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Labedan Bernard

2008-07-01

Full Text Available Abstract Background Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya, the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario. Results LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural

How old are chimpanzee communities? Time to the most recent common ancestor of the Y-chromosome in highly patrilocal societies.

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Langergraber, Kevin E; Rowney, Carolyn; Schubert, Grit; Crockford, Cathy; Hobaiter, Catherine; Wittig, Roman; Wrangham, Richard W; Zuberbühler, Klaus; Vigilant, Linda

2014-04-01

Many human societies are patrilineal, with males passing on their name or descent group affiliation to their offspring. Y-chromosomes are also passed on from father to son, leading to the simple expectation that males sharing the same surname or descent group membership should have similar Y-chromosome haplotypes. Although several studies in patrilineal human societies have examined the correspondence between Y-chromosome variation and surname or descent group membership, similar studies in non-human animals are lacking. Chimpanzees represent an excellent species for examining the relationship between descent group membership and Y-chromosome variation because they live in strongly male philopatric communities that arise by a group-fissioning process. Here we take advantage of recent analytical advances in the calculation of the time to the most recent common male ancestor and a large sample size of 273 Y-chromosome short tandem repeat haplotypes to inform our understanding of the potential ages of eight communities of chimpanzees. We find that the times to the most recent common male ancestor of chimpanzee communities are several hundred to as much as over two thousand years. These genetic estimates of the great time depths of chimpanzee communities accord well with behavioral observations suggesting that community fissions are a very rare event and are similar to genetic estimates of the time depth of patrilineal human groups. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor.

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Luo, Xin; Hu, Quanjun; Zhou, Pingping; Zhang, Dan; Wang, Qian; Abbott, Richard J; Liu, Jianquan

2017-06-01

Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a 'ghost' species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6-7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown 'ghost' tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs. © 2017 John Wiley & Sons Ltd.

Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

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Butzin, Nicholas C; Lapierre, Pascal; Green, Anna G; Swithers, Kristen S; Gogarten, J Peter; Noll, Kenneth M

2013-01-01

The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

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Nicholas C Butzin

Full Text Available The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS. These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

Convergent evolution of Hawaiian and Australo-Pacific honeyeaters from distant songbird ancestors.

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Fleischer, Robert C; James, Helen F; Olson, Storrs L

2008-12-23

The Hawaiian "honeyeaters," five endemic species of recently extinct, nectar-feeding songbirds in the genera Moho and Chaetoptila, looked and acted like Australasian honeyeaters (Meliphagidae), and no taxonomist since their discovery on James Cook's third voyage has classified them as anything else. We obtained DNA sequences from museum specimens of Moho and Chaetoptila collected in Hawaii 115-158 years ago. Phylogenetic analysis of these sequences supports monophyly of the two Hawaiian genera but, surprisingly, reveals that neither taxon is a meliphagid honeyeater, nor even in the same part of the songbird radiation as meliphagids. Instead, the Hawaiian species are divergent members of a passeridan group that includes deceptively dissimilar families of songbirds (Holarctic waxwings, neotropical silky flycatchers, and palm chats). Here we designate them as a new family, the Mohoidae. A nuclear-DNA rate calibration suggests that mohoids diverged from their closest living ancestor 14-17 mya, coincident with the estimated earliest arrival in Hawaii of a bird-pollinated plant lineage. Convergent evolution, the evolution of similar traits in distantly related taxa because of common selective pressures, is illustrated well by nectar-feeding birds, but the morphological, behavioral, and ecological similarity of the mohoids to the Australasian honeyeaters makes them a particularly striking example of the phenomenon.

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors [v1; ref status: indexed, http://f1000r.es/z6

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Thomas B Kepler

2013-04-01

Full Text Available One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the eliciting antigen. Advances in technology on several fronts have made it possible to clone large numbers of heavy-chain light-chain pairs from individual B cells and thereby identify whole sets of clonally related antibodies. These collections could provide the information necessary to reconstruct their own history - the sequence of changes introduced into the lineage during the development of the clone - and to study affinity maturation in detail. But the success of such a program depends entirely on accurately inferring the founding ancestor and the other unobserved intermediates. Given a set of clonally related immunoglobulin V-region genes, the method described here allows one to compute the posterior distribution over their possible ancestors, thereby giving a thorough accounting of the uncertainty inherent in the reconstruction. I demonstrate the application of this method on heavy-chain and light-chain clones, assess the reliability of the inference, and discuss the sources of uncertainty.

Aberrant Time to Most Recent Common Ancestor as a Signature of Natural Selection.

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Hunter-Zinck, Haley; Clark, Andrew G

2015-10-01

Natural selection inference methods often target one mode of selection of a particular age and strength. However, detecting multiple modes simultaneously, or with atypical representations, would be advantageous for understanding a population's evolutionary history. We have developed an anomaly detection algorithm using distributions of pairwise time to most recent common ancestor (TMRCA) to simultaneously detect multiple modes of natural selection in whole-genome sequences. As natural selection distorts local genealogies in distinct ways, the method uses pairwise TMRCA distributions, which approximate genealogies at a nonrecombining locus, to detect distortions without targeting a specific mode of selection. We evaluate the performance of our method, TSel, for both positive and balancing selection over different time-scales and selection strengths and compare TSel's performance with that of other methods. We then apply TSel to the Complete Genomics diversity panel, a set of human whole-genome sequences, and recover loci previously inferred to be under positive or balancing selection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Buoyancy differences among two deepwater ciscoes from the Great Lakes and their putative ancestor

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Krause, A.E.; Eshenroder, R.L.; Begnoche, L.J.

2002-01-01

We analyzed buoyancy in two deepwater ciscoes, Coregonus hoyi and C. kiyi, and in C. artedi, their putative ancestor, and also analyzed how variations in fish weight, water content, and lipid content affected buoyancy. Buoyancy was significantly different among the three species (p < 0.0001). Estimates of percent buoyancy (neutral buoyancy = 0.0%) were: kiyi, 3.8%; hoyi, 4.7%; and artedi, 5.7%. Buoyancy did not change with fish weight alone (p = 0.38). Fish weight was negatively related to water content for all three species (p = 0.037). Lipid content was not significantly different between hoyi and kiyi, but artedi had significantly fewer lipids than hoyi and kiyi (p < 0.10). When artedi was removed from the analysis, fish weight and lipids accounted for 48% of the variation in buoyancy (p = 0.003), fatter hoyi were less dense than leaner hoyi, but fatter and leaner kiyi were no different in density. Our findings provide additional evidence that buoyancy regulation was a speciating mechanism in deepwater ciscoes and that kiyi is more specialized than hoyi for diel-vertical migration in deep water.

Comparative high-resolution mapping of the wax inhibitors Iw1 and Iw2 in hexaploid wheat.

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Haibin Wu

Full Text Available The wax (glaucousness on wheat leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2 and non-glaucousness loci (Iw1 and Iw2. The non-glaucousness (Iw loci act as inhibitors of the glaucousness loci (W. High-resolution comparative genetic linkage maps of the wax inhibitors Iw1 originating from Triticum dicoccoides, and Iw2 from Aegilops tauschii were developed by comparative genomics analyses of Brachypodium, sorghum and rice genomic sequences corresponding to the syntenic regions of the Iw loci in wheat. Eleven Iw1 and eight Iw2 linked EST markers were developed and mapped to linkage maps on the distal regions of chromosomes 2BS and 2DS, respectively. The Iw1 locus mapped within a 0.96 cM interval flanked by the BE498358 and CA499581 EST markers that are collinear with 122 kb, 202 kb, and 466 kb genomic regions in the Brachypodium 5S chromosome, the sorghum 6S chromosome and the rice 4S chromosome, respectively. The Iw2 locus was located in a 4.1 to 5.4-cM interval in chromosome 2DS that is flanked by the CJ886319 and CJ519831 EST markers, and this region is collinear with a 2.3 cM region spanning the Iw1 locus on chromosome 2BS. Both Iw1 and Iw2 co-segregated with the BF474014 and CJ876545 EST markers, indicating they are most likely orthologs on 2BS and 2DS. These high-resolution maps can serve as a framework for chromosome landing, physical mapping and map-based cloning of the wax inhibitors in wheat.

Diversification of the celiac disease α-gliadin complex in wheat: a 33-mer peptide with six overlapping epitopes, evolved following polyploidization.

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Ozuna, Carmen V; Iehisa, Julio C M; Giménez, María J; Alvarez, Juan B; Sousa, Carolina; Barro, Francisco

2015-06-01

The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6-8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: p31-43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. Next-generation sequencing (NGS) and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1-6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31-43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only type 1 α-gliadins contained 33-mer epitopes. Moreover, the full immunodominant 33-mer fragment was only present in hexaploid wheat at low abundance, probably as the result of allohexaploidization events from subtype 1.2 α-gliadins found only in Aegilops tauschii, the D-genome donor of hexaploid wheat. Type 3 α-gliadins seem to be the ancestral type as they are found in most of the α-gliadin-expressing Triticeae species. These findings are important for reducing the incidence of CD by the breeding/selection of wheat varieties with low stimulatory capacity of T cells. Moreover, advanced genome-editing techniques (TALENs, CRISPR) will be easier to implement on the small group of α-gliadins containing only immunogenic peptides. © 2015 Society for Experimental Biology and John Wiley & Sons Ltd.

Analysis of the Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health-related traits of common wheat.

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Li, Da; Jin, Huaibing; Zhang, Kunpu; Wang, Zhaojun; Wang, Faming; Zhao, Yue; Huo, Naxin; Liu, Xin; Gu, Yong Q; Wang, Daowen; Dong, Lingli

2018-05-11

Gliadins are a major component of wheat seed proteins. However, the complex homoeologous Gli-2 loci (Gli-A2, -B2 and -D2) that encode the α-gliadins in commercial wheat are still poorly understood. Here we analyzed the Gli-D2 locus of Xiaoyan 81 (Xy81), a winter wheat cultivar. A total of 421.091 kb of the Gli-D2 sequence was assembled from sequencing multiple bacterial artificial clones, and 10 α-gliadin genes were annotated. Comparative genomic analysis showed that Xy81 carried only eight of the α-gliadin genes of the D genome donor Aegilops tauschii, with two of them each experiencing a tandem duplication. A mutant line lacking Gli-D2 (DLGliD2) consistently exhibited better breadmaking quality and dough functionalities than its progenitor Xy81, but without penalties in other agronomic traits. It also had an elevated lysine content in the grains. Transcriptome analysis verified the lack of Gli-D2 α-gliadin gene expression in DLGliD2. Furthermore, the transcript and protein levels of protein disulfide isomerase were both upregulated in DLGliD2 grains. Consistent with this finding, DLGliD2 had increased disulfide content in the flour. Our work sheds light on the structure and function of Gli-D2 in commercial wheat, and suggests that the removal of Gli-D2 and the gliadins specified by it is likely to be useful for simultaneously enhancing the end-use and health-related traits of common wheat. Because gliadins and homologous proteins are widely present in grass species, the strategy and information reported here may be broadly useful for improving the quality traits of diverse cereal crops. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

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Andrésdóttir Valgerdur

2008-11-01

Full Text Available Abstract Background APOBEC3 (A3 proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3. The presence of one A3 gene in mice (Z2–Z3 and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3, suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs. Results Sheep and cattle have three A3 genes, A3Z1, A3Z2 and A3Z3, whereas pigs only have two, A3Z2 and A3Z3. A comparison between domestic and wild pigs indicated that A3Z1 was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three A3 genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular A3 repertoire existed in the common ancestor of artiodactyls and primates (i.e., the ancestor of placental mammals. This mammalian ancestor therefore possessed the minimal A3 gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire. Conclusion The dynamic recombination-filled history of the mammalian A3 genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions were selected by ancient pathogenic retrovirus infections.

Population genetics of foxtail millet and its wild ancestor

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Wang Yongfang

2010-10-01

Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

"While we are questioning we are progressing"—A Reply to the Ancestors of Qualitative Research

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Monika Götsch

2009-07-01

Full Text Available REICHERTZ' reflections on the development of qualitative research during the Berlin Meeting on Qualitative Research Methods in 2009 (http://www.berliner-methodentreffen.de/ have led to the following central questions: Are we facing the end of critical social research? Is this possible end correlated with an uncritical mass of young scientists? In their reply to the ancestors of qualitative research the present authors advocate the abolition of a bipolar thinking about the issues and support a hybrid turn, standing the test through a fundamentally open-minded, reflexive, and deconstructive researcher`s attitude. Using the example of ethnography and gender studies we show that there are indeed opportunities for the future of critical social research: This approach would take place beyond the slaves of market-controlled contract research and ahead of the characters of the eternal hall of fame of social research. URN: urn:nbn:de:0114-fqs0903306

Mapping of stripe rust resistance gene in an Aegilops caudate introgression line in wheat and its genetic association with leaf rust resistance.

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Toor, Puneet Inder; Kaur, Satinder; Bansal, Mitaly; Yadav, Bharat; Chhuneja, Parveen

2016-12-01

A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distance of 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae during Incompatible Infection to Aegilops variabilis.

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Minghui Zheng

Full Text Available One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae. These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investigated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process, and three of which were significantly gene-enriched. Besides, the protein-protein interaction network analysis revealed 35 node unigenes which may play an important role in the plant-CCN interaction. Moreover, in a comparison of differentially expressed genes between the pre-parasitic juveniles and the early parasitic juveniles, we found that hydrolase activity was up-regulated in pre J2s whereas binding activity was upregulated in infective J2s. RT-qPCR analysis on some selected genes showed detectable expression, indicating possible secretion of the proteins and putative role in infection. This study provided better insights into the incompatible interaction between H. avenae and the host plant Ae. varabilis. Moreover, RNAi

The evolution of air resonance power efficiency in the violin and its ancestors.

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Nia, Hadi T; Jain, Ankita D; Liu, Yuming; Alam, Mohammad-Reza; Barnas, Roman; Makris, Nicholas C

2015-03-08

The fact that acoustic radiation from a violin at air-cavity resonance is monopolar and can be determined by pure volume change is used to help explain related aspects of violin design evolution. By determining the acoustic conductance of arbitrarily shaped sound holes, it is found that air flow at the perimeter rather than the broader sound-hole area dominates acoustic conductance, and coupling between compressible air within the violin and its elastic structure lowers the Helmholtz resonance frequency from that found for a corresponding rigid instrument by roughly a semitone. As a result of the former, it is found that as sound-hole geometry of the violin's ancestors slowly evolved over centuries from simple circles to complex f-holes, the ratio of inefficient, acoustically inactive to total sound-hole area was decimated, roughly doubling air-resonance power efficiency. F-hole length then slowly increased by roughly 30% across two centuries in the renowned workshops of Amati, Stradivari and Guarneri, favouring instruments with higher air-resonance power, through a corresponding power increase of roughly 60%. By evolution-rate analysis, these changes are found to be consistent with mutations arising within the range of accidental replication fluctuations from craftsmanship limitations with subsequent selection favouring instruments with higher air-resonance power.

Low-molecular-weight glutenin subunits from the 1U genome of Aegilops umbellulata confer superior dough rheological properties and improve breadmaking quality of bread wheat.

Science.gov (United States)

Wang, Jian; Wang, Chang; Zhen, Shoumin; Li, Xiaohui; Yan, Yueming

2018-04-01

Wheat-related genomes may carry new glutenin genes with the potential for quality improvement of breadmaking. In this study, we estimated the gluten quality properties of the wheat line CNU609 derived from crossing between Chinese Spring (CS, Triticum aestivum L., 2n = 6x = 42, AABBDD) and the wheat Aegilops umbellulata (2n = 2x = 14, UU) 1U(1B) substitution line, and investigated the function of 1U-encoded low-molecular-weight glutenin subunits (LMW-GS). The main quality parameters of CNU609 were significantly improved due to introgression of the 1U genome, including dough development time, stability time, farinograph quality number, gluten index, loaf size and inner structure. Glutenin analysis showed that CNU609 and CS had the same high-molecular-weight glutenin subunit (HMW-GS) composition, but CNU609 carried eight specific 1U genome-encoded LMW-GS. The introgression of the 1U-encoded LMW-GS led to more and larger protein body formation in the CNU609 endosperm. Two new LMW-m type genes from the 1U genome, designated Glu-U3a and Glu-U3b, were cloned and characterized. Secondary structure prediction implied that both Glu-U3a and Glu-U3b encode subunits with high α-helix and β-strand content that could benefit the formation of superior gluten structure. Our results indicate that the 1U genome has superior LMW-GS that can be used as new gene resources for wheat gluten quality improvement. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Strong gender differences in reproductive success variance, and the times to the most recent common ancestors.

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Favre, Maroussia; Sornette, Didier

2012-10-07

The Time to the Most Recent Common Ancestor (TMRCA) based on human mitochondrial DNA (mtDNA) is estimated to be twice that based on the non-recombining part of the Y chromosome (NRY). These TMRCAs have special demographic implications because mtDNA is transmitted only from mother to child, while NRY is passed along from father to son. Therefore, the former locus reflects female history, and the latter, male history. To investigate what caused the two-to-one female-male TMRCA ratio r(F/M)=T(F)/T(M) in humans, we develop a forward-looking agent-based model (ABM) with overlapping generations. Our ABM simulates agents with individual life cycles, including life events such as reaching maturity or menopause. We implemented two main mating systems: polygynandry and polygyny with different degrees in between. In each mating system, the male population can be either homogeneous or heterogeneous. In the latter case, some males are 'alphas' and others are 'betas', which reflects the extent to which they are favored by female mates. A heterogeneous male population implies a competition among males with the purpose of signaling as alpha males. The introduction of a heterogeneous male population is found to reduce by a factor 2 the probability of finding equal female and male TMRCAs and shifts the distribution of r(F/M) to higher values. In order to account for the empirical observation of the factor 2, a high level of heterogeneity in the male population is needed: less than half the males can be alphas and betas can have at most half the fitness of alphas for the TMRCA ratio to depart significantly from 1. In addition, we find that, in the modes that maximize the probability of having 1.5ancestors. We also tested the effect of sex-biased migration and sex-specific death rates and found that these are unlikely to explain alone the sex-biased TMRCA ratio observed in humans. Our results support the view

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

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Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

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Shah, Firoz; Nicolás, César; Bentzer, Johan; Ellström, Magnus; Smits, Mark; Rineau, Francois; Canbäck, Björn; Floudas, Dimitrios; Carleer, Robert; Lackner, Gerald; Braesel, Jana; Hoffmeister, Dirk; Henrissat, Bernard; Ahrén, Dag; Johansson, Tomas; Hibbett, David S; Martin, Francis; Persson, Per; Tunlid, Anders

2016-03-01

Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Wild mallards have more "goose-like" bills than their ancestors: a case of anthropogenic influence?

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Pär Söderquist

Full Text Available Wild populations of the world's most common dabbling duck, the mallard (Anas platyrhynchos, run the risk of genetic introgression by farmed conspecifics released for hunting purposes. We tested whether bill morphology of free-living birds has changed since large-scale releases of farmed mallards started. Three groups of mallards from Sweden, Norway and Finland were compared: historical wild (before large-scale releases started, present-day wild, and present-day farmed. Higher density of bill lamellae was observed in historical wild mallards (only males. Farmed mallards had wider bills than present-day and historical wild ones. Present-day wild and farmed mallards also had higher and shorter bills than historical wild mallards. Present-day mallards thus tend to have more "goose-like" bills (wider, higher, and shorter than their ancestors. Our study suggests that surviving released mallards affect morphological traits in wild population by introgression. We discuss how such anthropogenic impact may lead to a maladapted and genetically compromised wild mallard population. Our study system has bearing on other taxa where large-scale releases of conspecifics with 'alien genes' may cause a cryptic invasive process that nevertheless has fitness consequences for individual birds.

Quality of synthetic hexaploid wheat containing null alleles at Glu-A1

Indian Academy of Sciences (India)

GSs. However, incorporation of HMW-GS from Ae. tauschii in six synthetic hexaploid wheat lines significantly increased most quality related parameters. The potential values of these wheat lines in improving the quality of wheat are discussed.

Divergence in homoeolog expression of the grain length-associated gene GASR7 during wheat allohexaploidization

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Dongdong Zhang

2015-02-01

Full Text Available Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent (Triticum turgidum, AABB, PI 94655 in contrast to the round seed shape of its paternal progenitor (Aegilops tauschii, DD, AS2404. We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid (GA response elements, with the TaGASR7B promoter (pTaGASR7B uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaGASR7B. McrBC enzyme assays showed that the methylation status at pTaGASR7D was increased during allohexaploidization, consistent with the repressed expression of TaGASR7D. For pTaGASR7A, the distribution of repetitive sequence-derived 24-nucleotide (nt small interfering RNAs (siRNAs were found which suggests possible epigenetic regulation because 24-nt siRNAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.

The cult of amphioxus in German Darwinism; or, our gelatinous ancestors in Naples' blue and balmy bay.

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Hopwood, Nick

2015-01-01

Biologists having rediscovered amphioxus, also known as the lancelet or Branchiostoma, it is time to reassess its place in early Darwinist debates over vertebrate origins. While the advent of the ascidian-amphioxus theory and challenges from various competitors have been, documented, this article offers a richer account of the public appeal of amphioxus as a primitive ancestor. The focus is on how the 'German Darwin' Ernst Haeckel persuaded general magazine and newspaper readers to revere this "flesh of our flesh and blood of our blood", and especially on Das neue Laienbrevier des Haeckelismus (The new lay breviary of Haeckelism) by Moritz Reymond with cartoons by Fritz Steub. From the late 1870s these successful little books of verse introduced the Neapolitan discoveries that made the animal's name and satirized Haeckel's rise as high priest of its cult. One song is reproduced and translated here, with a contemporary "imitation" by the Canadian palaeontologist Edward John Chapman, and extracts from others. Predating the American "It's a long way from amphioxus" by decades, these rhymes dramatize neglected 'species politics' of Darwinism and highlight the roles of humour in negotiating evolution.

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species

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Hong-Ying Jian

2018-02-01

Full Text Available Rosa chinensis var. spontanea, an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC region of 85,910 bp and one small single copy (SSC region of 18,762 bp, separated by two inverted repeat (IR regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs, 37 transfer RNA (tRNA genes, and eight ribosomal RNA (rRNA genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. spontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses. This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa, and it might also

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species.

Science.gov (United States)

Jian, Hong-Ying; Zhang, Yong-Hong; Yan, Hui-Jun; Qiu, Xian-Qin; Wang, Qi-Gang; Li, Shu-Bin; Zhang, Shu-Dong

2018-02-12

Rosa chinensis var. spontanea , an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp) genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC) region of 85,910 bp and one small single copy (SSC) region of 18,762 bp, separated by two inverted repeat (IR) regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. s pontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses . This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa , and it might also facilitate the

The proteomic complexity and rise of the primordial ancestor of diversified life

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Kim Kyung

2011-05-01

Full Text Available Abstract Background The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations. Results Here we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation. Conclusions The minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the

Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae.

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Barker, Michael S; Li, Zheng; Kidder, Thomas I; Reardon, Chris R; Lai, Zhao; Oliveira, Luiz O; Scascitelli, Moira; Rieseberg, Loren H

2016-07-01

Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature. We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy. We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia. Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and that most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels. © 2016 Botanical Society of America.

Genetic Fingerprinting of Wheat and Its Progenitors by Mitochondrial Gene orf256

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Mona M. Elseehy

2012-04-01

Full Text Available orf256 is a wheat mitochondrial gene associated with cytoplasmic male sterility (CMS that has different organization in various species. This study exploited the orf256 gene as a mitochondrial DNA marker to study the genetic fingerprint of Triticum and Aegilops species. PCR followed by sequencing of common parts of the orf256 gene were employed to determine the fingerprint and molecular evolution of Triticum and Aegilops species. Although many primer pairs were used, two pairs of orf256 specific primers (5:-94/C: 482, 5:253/C: 482, amplified DNA fragments of 576 bp and 230 bp respectively in all species were tested. A common 500 bp of nine species of Triticum and Aegilops were aligned and showed consistent results with that obtained from other similar chloroplast or nuclear genes. Base alignment showed that there were various numbers of base substitutions in all species compared to S. cereal (Sc (the outgroup species. Phylogenetic relationship revealed similar locations and proximity on phylogenetic trees established using plastid and nuclear genes. The results of this study open a good route to use unknown function genes of mitochondria in studying the molecular relationships and evolution of wheat and complex plant genomes.

Джерела стійкості проти збудника бурої іржі та їх використання у процесі створення сортів пшениці м’якої

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Г. М. Ковалишина

2017-12-01

�еному пшениці та її родичів ідентифіковано й охарактеризовано за хромосомною локалізацією та ефективністю понад 90 (Lr генів стійкості проти цього збудника. Виявлено, що майже всі ефективні на території України гени стійкості проти збудника бурої іржі, окрім Lr10 та Lr23, є чужорідними, перенесеними в Triticum aestivum від інших видів: Aegilops speltoides – гени Lr28, Lr35, Lr36, Lr47, Lr51, Lr66; Aegilops tauschii – Lr1, Lr21, Lr22а, Lr32, Lr39, Lr42; Triticum timopheevii – Lr18 та Lr50; Thinopyrum elongatum – Lr19, Lr29, Lr24; Secale cereale – Lr25, Lr26 та Lr45; Aegilops umbellulata – Lr9, Lr76; Triticum speltа – Lr44, Lr65, Lr71; Triticum dicoccoides – Lr53, Lr64; Aegilops triuncialis – Lr58, LrTr; Tr. timopheevii spp. viticulosum – LrTt1; Aegilops ventricosa – Lr37; Aegilops kotschyi – Lr54; Elymus trachycaulis – Lr55; Aegilops sharonensis – Lr56; Aegilops geniculate – Lr57; Aegilops peregrine – Lr59; Triticum turgidum – Lr61; Aegilops neglecta – Lr62; Triticum monococcum – Lr63. Висновки. Залучення до схрещувань культурних та диких видів родичів пшениці дасть змогу отримати неоднорідний за стійкістю проти збудника бурої іржі селекційний матеріал.

tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor.

Science.gov (United States)

Qu, Ge; Wang, Wei; Chen, Ling-Ling; Qian, Shao-Song; Zhang, Hong-Yu

2009-10-01

Although cysteine (Cys) is beneficial to stabilize protein structures, it is not prevalent in thermophiles. For instance, the Cys contents in most thermophilic archaea are only around 0.7%. However, methanogenic archaea, no matter thermophilic or not, contain relatively abundant Cys, which remains elusive for a long time. Recently, Klipcan et al. correlated this intriguing property of methanogenic archaea with their unique tRNA-dependent Cys biosynthetic pathway. But, the deep reasons underlying the correlation are ambiguous. Considering the facts that free Cys is thermally labile and the tRNA-dependent Cys biosynthesis avoids the use of free Cys, we speculate that the unique Cys biosynthetic pathway represents a strategy to increase Cys contents by preventing it from thermal degradation, which may be relevant to the thermal adaptation of methanogenic archaea ancestor.

The γ-gliadin multigene family in common wheat (Triticum aestivum and its closely related species

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Chen Qing

2009-04-01

Full Text Available Abstract Background The unique properties of wheat flour primarily depend on gluten, which is the most important source of protein for human being. γ-Gliadins have been considered to be the most ancient of the wheat gluten family. The complex family structure of γ-gliadins complicates the determination of their function. Moreover, γ-gliadins contain several sets of celiac disease epitopes. However, no systematic research has been conducted yet. Results A total of 170 γ-gliadin genes were isolated from common wheat and its closely related species, among which 138 sequences are putatively functional. The ORF lengths of these sequences range from 678 to 1089 bp, and the repetitive region is mainly responsible for the size heterogeneity of γ-gliadins. The repeat motif P(Q/L/S/T/I/V/R/AF(S/Y/V/Q/I/C/LP(R/L/S/T/H/C/YQ1–2(P(S/L/T/A/F/HQQ1–2is repeated from 7 to 22 times. Sequence polymorphism and linkage disequilibrium analyses show that γ-gliadins are highly diverse. Phylogenic analyses indicate that there is no obvious discrimination between Sitopsis and Ae. tauschii at the Gli-1 loci, compared with diploid wheat. According to the number and placement of cysteine residues, we defined nine cysteine patterns and 17 subgroups. Alternatively, we classified γ-gliadins into two types based on the length of repetitive domain. Amino acid composition analyses indicate that there is a wide range of essential amino acids in γ-gliadins, and those γ-gliadins from subgroup SG-10 and SG-12 and γ-gliadins with a short repetitive domain are more nutritional. A screening of toxic epitopes shows that γ-gliadins with a pattern of C9 and γ-gliadins with a short repetitive domain almost lack any epitopes. Conclusion γ-Gliadin sequences in wheat and closely related Aegilops species are diverse. Each group/subgroup contributes differently to nutritional quality and epitope content. It is suggested that the genes with a short repetitive domain are more

RFLP of analyses of an intergenic spacer region of chloroplast DNA ...

African Journals Online (AJOL)

African Journal of Biotechnology. Journal Home · ABOUT ... In this study, 11 wheat species of Triticum and. Aegilops were ... and a phenogram was constructed using SAHN clustering unweighted pair group method using arithmetic averages.

Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species

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Lovley Derek R

2009-03-01

Full Text Available Abstract Background The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. Results In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer. Conclusion The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.

Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple.

Science.gov (United States)

Ma, X; Cai, Z; Liu, W; Ge, S; Tang, L

2017-09-01

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.

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Jonathan L Gordon

2009-05-01

Full Text Available Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, to infer the gene content and gene order that existed in the genome of an extinct ancestral yeast about 100 Mya, immediately before it underwent whole-genome duplication (WGD. The reconstructed ancestral genome contains 4,703 ordered loci on eight chromosomes. The reconstruction is complete except for the subtelomeric regions. We then inferred the series of rearrangement steps that led from this ancestor to the current Saccharomyces cerevisiae genome; relative to the ancestral genome we observe 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. Some fragile chromosomal sites were reused as evolutionary breakpoints multiple times. We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, including one that is derived from a hAT family transposon, and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD. Sites of gene gain and evolutionary breakpoints both tend to be associated with tRNA genes and, to a lesser extent, with origins of replication. Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources.

Characterization of low-molecular-weight glutenin subunit genes of ...

Indian Academy of Sciences (India)

2015-09-16

Sep 16, 2015 ... 4Ministry of Education, Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, ... gene mining have also been conducted in Aegilops genus, ... sites and pair-wise deletion for gaps/missing data.

A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease

DEFF Research Database (Denmark)

Forsberg, Roald; Oleksiewicz, Martin B.; Krabbe Petersen, Anne Mette

2001-01-01

an accurate molecular clock for the European PRRSV ORF 3 gene, place the root in the genealogy, estimate the rate of nucleotide substitution, and date the most recent common viral ancestor of the data set to 1979; more than 10 years before the onset of the European epidemic. Based on these findings, we...... conclude that PRRSV virus most likely entered the pig population some time before the epidemic emergence of the virus, and hence, that emergence of European-type PRRSV is not the result of a recent species transmission event. Together, our results show that ORF3 sequencing is a valuable epidemiologic tool...... for examining the emergence and spread of PRRSV in Europe. As such, the panel of well-characterized and highly divergent ORF3 sequences described in this study provides a reference point for future molecular epidemiologic studies....

Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov. Part I. Nicolae Milescu-Spătarul’s secular European impact; 1st of June 2011 - 375 years since the birth of the European erudite

Directory of Open Access Journals (Sweden)

Dan RIGA

2011-01-01

Full Text Available The culture of tradition and patrimony is an act of civilization, as well as one of identitaryeducation. This is why the promotion of restitution comprises all areas of progress and humancreation.Nicolae Milescu-Spătarul (b. 1636 in Moldavia - d. 1708 in Russia was an eruditehumanist scholar, an encyclopaedist, a theologist, diplomat, historian, geographer, ethnographer,translator, memorialist and a polyglot (Romanian, ancient and modern Greek, Latin, Turkish andSlavonic-Russian. Commemorating and honouring this figure, of European and Eurasianimportance alike, is a debt of honour: 1958 – 250 years since death; 2011 – 375 years since birth.At this time, the need to fully publish his work arises, as a large part of it is still kept in libraries,archives and European private collections in the form of manuscripts. Nicolae Milescu-Spătarulwas the ancestor of the Nobel Laureate (1908, scientist Ilia I. Mecinikov (1845-1916.The work reveals the great scholar’s (eastern, but also western, European and Asiancultural, scientific and diplomatic impact – at that moment and throughout time – but also theSorin Riga, Dan Riga, Vasile Man - Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov impact of his vast work. The remarkable monograph The Description of China (58 chapters was published in Romanian only in 1958.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Molecular cloning and functional characterization of two novel high molecular weight glutenin subunit genes in Aegilops markgrafii ..... Distinct classical and molecular cytogenetics of Astyanax marionae and A. fasciatus ... Clinical utility of a 377 gene custom next-generation sequencing epilepsy panel .... Contact | Site index.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

Science.gov (United States)

Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics. XIAOCUN ZHANG. Articles written in Journal of Genetics. Volume 96 Issue 4 September 2017 pp 563-570 RESEARCH ARTICLE. Molecular cloning and functional characterization of two novel high molecular weight glutenin subunit genes in Aegilops markgrafii · XUYE DU XIAOCUN ...

Cell-Specific Expression of Homospermidine Synthase, the Entry Enzyme of the Pyrrolizidine Alkaloid Pathway in Senecio vernalis, in Comparison with Its Ancestor, Deoxyhypusine Synthase1

Science.gov (United States)

Moll, Stefanie; Anke, Sven; Kahmann, Uwe; Hänsch, Robert; Hartmann, Thomas; Ober, Dietrich

2002-01-01

Pyrrolizidine alkaloids (PAs) are constitutive plant defense compounds with a sporadic taxonomic occurrence. The first committed step in PA biosynthesis is catalyzed by homospermidine synthase (HSS). Recent evidence confirmed that HSS evolved by gene duplication from deoxyhypusine synthase (DHS), an enzyme involved in the posttranslational activation of the eukaryotic translation initiation factor 5A. To better understand the evolutionary relationship between these two enzymes, which are involved in completely different biological processes, we studied their tissue-specific expression. RNA-blot analysis, reverse transcriptase-PCR, and immunolocalization techniques demonstrated that DHS is constitutively expressed in shoots and roots of Senecio vernalis (Asteraceae), whereas HSS expression is root specific and restricted to distinct groups of endodermis and neighboring cortex cells located opposite to the phloem. All efforts to detect DHS by immunolocalization failed, but studies with promoter-β-glucuronidase fusions confirmed a general expression pattern, at least in young seedlings of tobacco (Nicotiana tabacum). The expression pattern for HSS differs completely from its ancestor DHS due to the adaptation of HSS to the specific requirements of PA biosynthesis. PMID:12226485

Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum.

Science.gov (United States)

Armijos Jaramillo, Vinicio Danilo; Vargas, Walter Alberto; Sukno, Serenella Ana; Thon, Michael R

2013-01-01

The genus Colletotrichum contains a large number of phytopathogenic fungi that produce enormous economic losses around the world. The effect of horizontal gene transfer (HGT) has not been studied yet in these organisms. Inter-Kingdom HGT into fungal genomes has been reported in the past but knowledge about the HGT between plants and fungi is particularly limited. We describe a gene in the genome of several species of the genus Colletotrichum with a strong resemblance to subtilisins typically found in plant genomes. Subtilisins are an important group of serine proteases, widely distributed in all of the kingdoms of life. Our hypothesis is that the gene was acquired by Colletotrichum spp. through (HGT) from plants to a Colletotrichum ancestor. We provide evidence to support this hypothesis in the form of phylogenetic analyses as well as a characterization of the similarity of the subtilisin at the primary, secondary and tertiary structural levels. The remarkable level of structural conservation of Colletotrichum plant-like subtilisin (CPLS) with plant subtilisins and the differences with the rest of Colletotrichum subtilisins suggests the possibility of molecular mimicry. Our phylogenetic analysis indicates that the HGT event would have occurred approximately 150-155 million years ago, after the divergence of the Colletotrichum lineage from other fungi. Gene expression analysis shows that the gene is modulated during the infection of maize by C. graminicola suggesting that it has a role in plant disease. Furthermore, the upregulation of the CPLS coincides with the downregulation of several plant genes encoding subtilisins. Based on the known roles of subtilisins in plant pathogenic fungi and the gene expression pattern that we observed, we postulate that the CPLSs have an important role in plant infection.

SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory.

Science.gov (United States)

Gouilh, Meriadeg Ar; Puechmaille, Sébastien J; Gonzalez, Jean-Paul; Teeling, Emma; Kittayapong, Pattamaporn; Manuguerra, Jean-Claude

2011-10-01

phylogeny and the host/pathogen ecological interactions in the description and the understanding of pathogen emergence. The host's phylogeny, biogeography and behaviour, combined with already described roles of pathogen plasticity and anthropic changes are likely to be co-factors of disease emergence. Elucidating the common ancestor of Hipposideridae and Rhinolophidae is key to understanding the evolutionary history of actual betacoronaviruses and therefore to get an insight of the deep origin of SARS-CoV. Copyright © 2011 Elsevier B.V. All rights reserved.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics. PARVEEN CHHUNEJA. Articles written in Journal of Genetics. Volume 91 Issue 2 August 2012 pp 155-161 Research Article. Introgression of a leaf rust resistance gene from Aegilops caudata to bread wheat · Amandeep Kaur Riar Satinder Kaur H. S. Dhaliwal Kuldeep Singh Parveen ...

Molecular and cytogenetic characterization of wheat introgression lines carrying the stem rust resistance gene Sr39.

Science.gov (United States)

Stem rust, caused by Puccinia graminis Pers.:Pers. f.sp. tritici Eriks. and Henn., poses a serious threat to global wheat production because of the emergence of Pgt-TTKSK (Ug99). The TTKSK resistant gene Sr39 was derived from Aegilops speltoides through chromosome translocation. In this study, we ch...

From the Cult of the “Self” to the Ancestor Cult: Trilogy The Cult of the Self by Maurice Barrés

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Vera V. Shervashidze

2016-09-01

Full Text Available The debut of Maurice Barrès, his trilogy The Cult of the Self immediately won the reader’s attention. In the 1890s, his works evoked increasing interest. His contemporaries read them as a fascinating narrative about the drama of European consciousness and the attempts to overcome this drama. However, after the author’s death, the interest of readers and researchers to his works decreased that may be explained by his fascination with ideas of nationalism, or boulangisme, especially during the war. The writer was accused of nationalism, however his nationalism was but a “replica” of his early ideas about the “culture” of “the self.” According to Barrès, all major themes of his work were reflected in the first trilogy of The Cult of the Self. Later in his career, revealing the typological similarity of the processes taking place in the inner “self” and within the nation, he wrote about degradation of the “self” and degradation of the nation in parallel. Portraying “the disease of the century” and seeking its recovery, Barrès introduced the theme of the ancestor cult as a means of moral redemption in his late work. The present study of linguistic, cultural, and historical properties of Barrès’s work intends to introduce one of the greatest turn-of-the-century writers into the Russian academic context.

The Ancestor as Subtext

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Sabine Broeck

2009-06-01

Full Text Available This text has grown out of my love of and respect for Toni Morrison's work. It is supposed to be−however much it might take the shape of a critical reading−very much my homage to the work of a writer who has made some of the most articulate and publicly visible moves to satisfy a communal desire for the African-American memory, and to create, if sites of stone and marble have been lacking, fictional spaces as "monuments" to the black diaspora in the New World. It is also a piece of work that ...

Whakaora nga moemoea o nga tupuna--living the dreams of the ancestors. Future planning in a Kaupapa Māori CAMHS team.

Science.gov (United States)

Elder, Hinemoa; Milne, Moe; Witehira, Heemi; Mendes, Patrick; Heslin, Anneliese; Cribb-Su'a, Ainsleigh; Wilson, Riwai; Goldsmith, Arona; Kainamu, Reena; Barrett, Moana; Love, Shar; Cargo, Tania; Kalra, Vanitha

2009-08-01

The aim of this study was to identify and operationalize aspects of a future planning process for sustainable delivery of Kaupapa Māori (Specialist Māori) mental health from a team called He Kakano, within Child and Adolescent Mental Health Services in South Auckland, New Zealand. A 2-day hui (meeting) was held with members of the team and a facilitator, Whaea Moe Milne. Review of background national epidemiological data, local data, information from community, carer and tangata whaiora (consumer) stakeholders and the existing He Kakano Model of Care was undertaken. Use of tikanga (Māori protocol and practices) was evident throughout the hui. A number of aspects of tikanga were identified as essential to the positive outcomes of the future plan. This paper reports one in particular, that of whakatauakī (proverbs where the originator is known). "Whakaora nga moemoea o nga tupuna--living the dreams of the ancestors" is a whakatauakī articulated by Whaea Moe Milne, which was identified as helpful in influencing the strategic planning thinking and decision-making process for He Kakano. This whakatauakī enabled the identification of shared goals, values, beliefs, behaviours and an action plan. The existing and ongoing relationship with Whaea Moe Milne was identified as an important element in the way in which the whakatauakī was received and reflected on. Use of tikanga Māori, in this case, whakatauakī, was helpful in developing future planning for He Kakano. This suggests that use of tikanga may be beneficial in other settings where planning for sustainable Māori responsive services is undertaken. Further work in this area is likely to benefit service development, strategic planning, workforce development and have an impact on improving health outcomes for Māori.

The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

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Brochier-Armanet Céline

2011-09-01

Full Text Available Abstract Background The Anaphase Promoting Complex or Cyclosome (APC/C is the largest member of the ubiquitin ligase [E3] family. It plays a crucial role in the control of the cell cycle and cell proliferation by mediating the proteolysis of key components by the proteasome. APC/C is made of a dozen subunits that assemble into a large complex of ~1.5 MDa, which interacts with various cofactors and targets. Results Using comparative genomic and phylogenetic approaches, we showed that 24 out of 37 known APC/C subunits, adaptors/co-activators and main targets, were already present in the Last Eukaryotic Common Ancestor (LECA and were well conserved to a few exceptions in all present-day eukaryotic lineages. The phylogenetic analysis of the 24 components inferred to be present in LECA showed that they contain a reliable phylogenetic signal to reconstruct the phylogeny of the domain Eucarya. Conclusions Taken together our analyses indicated that LECA had a complex and highly controlled modern-like cell cycle. Moreover, we showed that, despite what is generally assumed, proteins involved in housekeeping cellular functions may be a good complement to informational genes to study the phylogeny of eukaryotes.

Some ancestors of contraction analysis

DEFF Research Database (Denmark)

Jouffroy, Jerome

2005-01-01

Contraction analysis is a recent tool for analyzing the convergence behavior of nonlinear systems in state-space form (see Lohmiller and Slotine [16] for the main reference). However, it seems that earlier results derived by mathematicians in the 1950s closely match some of the results of contrac......Contraction analysis is a recent tool for analyzing the convergence behavior of nonlinear systems in state-space form (see Lohmiller and Slotine [16] for the main reference). However, it seems that earlier results derived by mathematicians in the 1950s closely match some of the results...

Sundials: Ancestors of Our Clocks

Indian Academy of Sciences (India)

ing in mathematics and astronomy, the Greeks, the Egyptians and the Babylonians constructed ... have knowledge about some of the basic concepts and terminolo- gies in astronomy. .... Treloars College, Hamp- shire, England. Courtesy: ...

Viral ancestors of antiviral systems.

Science.gov (United States)

Villarreal, Luis P

2011-10-01

All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.

Viral Ancestors of Antiviral Systems

Directory of Open Access Journals (Sweden)

Luis P. Villarreal

2011-10-01

Full Text Available All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.

Sequence diversity and copy number variation of Mutator-like transposases in wheat

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Nobuaki Asakura

2008-01-01

Full Text Available Partial transposase-coding sequences of Mutator-like elements (MULEs were isolated from a wild einkorn wheat, Triticum urartu, by degenerate PCR. The isolated sequences were classified into a MuDR or Class I clade and divided into two distinct subclasses (subclass I and subclass II. The average pair-wise identity between members of both subclasses was 58.8% at the nucleotide sequence level. Sequence diversity of subclass I was larger than that of subclass II. DNA gel blot analysis showed that subclass I was present as low copy number elements in the genomes of all Triticum and Aegilops accessions surveyed, while subclass II was present as high copy number elements. These two subclasses seemed uncapable of recognizing each other for transposition. The number of copies of subclass II elements was much higher in Aegilops with the S, Sl and D genomes and polyploid Triticum species than in diploid Triticum with the A genome, indicating that active transposition occurred in S, Sl and D genomes before polyploidization. DNA gel blot analysis of six species selected from three subfamilies of Poaceae demonstrated that only the tribe Triticeae possessed both subclasses. These results suggest that the differentiation of these two subclasses occurred before or immediately after the establishment of the tribe Triticeae.

Dataset of the HOX1 gene sequences of the wheat polyploids and their diploid relatives

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Andrey B. Shcherban

2018-02-01

Full Text Available The TaHOX-1 gene of common wheat Triticum aestivum L. (BAD-genome encodes transcription factor (HD-Zip I which is characterized by the presence of a DNA-binding homeodomain (HD with an adjacent Leucine zipper (LZ motif. This gene can play a role in adapting plant to a variety of abiotic stresses, such as drought, cold, salinity etc., which strongly affect wheat production. However, it's both functional role in stress resistance and divergence during wheat evolution has not yet been elucidated. This data in brief article is associated with the research paper “Structural and functional divergence of homoeologous copies of the TaHOX-1 gene in polyploid wheats and their diploid ancestors”. The data set represents a recent survey of the primary HOX-1 gene sequences isolated from the first wheat allotetraploids (BA-genome and their corresponding Triticum and Aegilops diploid relatives. Specifically, we provide detailed information about the HOX-1 nucleotide sequences of the promoter region and both nucleotide and amino acid sequences of the gene. The sequencing data used here is available at DDBJ/EMBL/GenBank under the accession numbers MG000630-MG000698. Keywords: Wheat, Polyploid, HOX-1 gene, Homeodomain, Transcription factor, Promoter, Triticum, Aegilops

Novel genetic diversity of the alien D-genome synthetic hexaploid wheat (2n=6x=42, Aabbdd) germplasm for various phenology traits

International Nuclear Information System (INIS)

Masood, R.M.; Bibi, K.; Jamil, M.

2016-01-01

The current study evaluates genetic penetrance and expressivity of an alien genome introgression in a set of 117 primary synthetic hexaploid wheat (SHW) accessions. These SHW have originated from durum wheat /accessions with three sets of durum wheat cultivars ALTAR 84, D67.2 and CERCETA as the female and diverse Ae. tauschii accessions as the pollen parents. Diversity of the 12 important traits (Growth habit, pigmentation, chlorophyll content, leaf area index, crop digital ground cover, awn size, awn length, and several seed digital imaging parameters)revealed significant variation for the respective traits, leading to the conclusion that Ae. tauschii accessions have tremendous diversity than the durum controls. Further, the value deviations within each attribute had a range of being lower or higher than their durum wheat female parents and these observations allowed us to use the variations as selective sieves and narrow down the desirable SHW that would be advantageous to exploit for wheat breeding and cultivar improvement programs. Selections were made and a group of 41SHW accessions were identified that will after an intermediate DNA diversity evaluation form a crisper final set for user friendly utilization. The range of selections shows multiple trait advantages for exploitation in both irrigated and rain-fed conditions. This pivotal study sets the foundation to better define the D genome SHW for efficient utilization in future research investigations. Our results have implications in widening the genetic base of hexaploid bread wheat and may facilitate the development of agronomically desirable wheat cultivars. (author)

The evolutive aspect of the short jat substituents following the sonant r - a comparison between the Serbian literary language and the dialect of Vuk’s ancestors

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Ostojić Vladimir B.

2015-01-01

Full Text Available The paper discusses the evolutive aspects of short “jat” following the sonant r usage during the formation of the modern Serbian literary language and its treatment in the Serbo-Croatistic and the Serbistic descriptive and normative literature. In addition to the basic issue of the distribution of the short “jat’s” substituent following the sonant r in dialects of Montenegro, particularly in the native dialect of Vuk Karadžić’s ancestors, the author also addresses the question related to the mechanisms that cause short “jat” following the sonant r in ijekavian dialects to be reduced sometimes to e, and sometimes to je. Substitution of short “jat” following the sonant r in Jezera-Šarani dialect had important evolution from the times of “classical Vukovian ijekavism”. In this dialect, forms with rje do not occur, except in the word starješina. Here, r and j remained in the same syllable, which set the stage for iotization and depalatalization. The analysis of the paper describes the situation in Jezera-Šarani dialect as well as the situation in other Montenegrian dialects of the older and newer Eastern-Herzegovian type. The author as well takes into consideration that our Pravopis has already disregarded the Vukovian tradition with omitting j that follows sonant r in the examples pogreška and greška. In order to eliminate the disunity, the author concludes that the status of the group re should not be questioned from the aspect of literary language standards.

Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov. Part II. Ilia I. Mecinikov’s life and scientific work; 16th of May 2011 - 166 years since the birth of the European scholar; 15th of July 2011 - 95 years since death

Directory of Open Access Journals (Sweden)

Dan RIGA

2011-01-01

Full Text Available The work showcases the promotion of Romanian lineage - Nicolae Milescu Spătarul (1636-1708 as ancestor of scientist Ilia Ilici Mecinikov (1845-1916, Nobel Laureate (1908.A great figure in world science and bio-medicine, the scientist - creator of two new modernsciences (immunology and gerontology – is claimed and honoured by four nations: Israeli, French,Russian and Ukrainian. Despite his known Romanian descent on his paternal side – biographicallyconsecrated by his wife Olga Mecinikov – Romania has pushed him into oblivion, by not promotingthis historical truth and reality to all.In our country, Prof. Dr. doc. Ilie Th. Riga (1908-1977 publishes in 1930, in the Romanianmagazine, Natura (Nature, Originea românească a lui Metchnikoff (Metchnikoff’s Romanianorigins. In the 2007-2011 period, two of the authors of the work continuously publish, in thecountry and abroad, thus creating Dosarul ascendenţei româneşti al lui Mecinikov (Mecinikov’sfile on his Romanian lineage, for the global informational civilization. They published their worksin printed version: in scientific magazines (2007, 2011, in their own monograph Medicina antiîmbătrânireşi ştiinţele longevităţii (Anti-aging Medicine and Longevity Sciences, (2007, innewspapers Ziua USA (The Day - USA, (2008 and Clipa. Magazinul Actualităţii CulturaleRomâneşti (The Moment. The Romanian Cultural Current Affairs Magazine, (2011, inEnciclopedia medicală Românească (Encyclopaedia of Romanian Medicine, (2009 and also onSorin Riga, Dan Riga, Vasile Man - Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov...250webpages (the online era: www.DacoRomanica.ro (2010, www.revista-studii-uvvg.ro (2011,www.ziuausa.com (2008, www.revistaclipa.com (2011, taken over by other internet websites.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

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Wolf Yuri I

2012-12-01

Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

The calmodulin-binding, short linear motif, NSCaTE is conserved in L-type channel ancestors of vertebrate Cav1.2 and Cav1.3 channels.

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Valentina Taiakina

Full Text Available NSCaTE is a short linear motif of (xWxxx(I or Lxxxx, composed of residues with a high helix-forming propensity within a mostly disordered N-terminus that is conserved in L-type calcium channels from protostome invertebrates to humans. NSCaTE is an optional, lower affinity and calcium-sensitive binding site for calmodulin (CaM which competes for CaM binding with a more ancient, C-terminal IQ domain on L-type channels. CaM bound to N- and C- terminal tails serve as dual detectors to changing intracellular Ca(2+ concentrations, promoting calcium-dependent inactivation of L-type calcium channels. NSCaTE is absent in some arthropod species, and is also lacking in vertebrate L-type isoforms, Cav1.1 and Cav1.4 channels. The pervasiveness of a methionine just downstream from NSCaTE suggests that L-type channels could generate alternative N-termini lacking NSCaTE through the choice of translational start sites. Long N-terminus with an NSCaTE motif in L-type calcium channel homolog LCav1 from pond snail Lymnaea stagnalis has a faster calcium-dependent inactivation than a shortened N-termini lacking NSCaTE. NSCaTE effects are present in low concentrations of internal buffer (0.5 mM EGTA, but disappears in high buffer conditions (10 mM EGTA. Snail and mammalian NSCaTE have an alpha-helical propensity upon binding Ca(2+-CaM and can saturate both CaM N-terminal and C-terminal domains in the absence of a competing IQ motif. NSCaTE evolved in ancestors of the first animals with internal organs for promoting a more rapid, calcium-sensitive inactivation of L-type channels.

Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization.

Science.gov (United States)

Yang, Guanghui; Liu, Zhenshan; Gao, Lulu; Yu, Kuohai; Feng, Man; Yao, Yingyin; Peng, Huiru; Hu, Zhaorong; Sun, Qixin; Ni, Zhongfu; Xin, Mingming

2018-01-01

Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent of origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid ( Aegilops spp), tetraploid, and hexaploid wheat ( Triticum spp) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene Ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Nearly half of the imprinted genes exhibited conserved expression patterns during wheat hexaploidization. In addition, 40% of the homoeolog pairs originating from whole-genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. These results suggest that genomic imprinting was evolutionarily conserved between closely related Triticum and Aegilops species and in the face of polyploid hybridization between species in these genera. © 2018 American Society of Plant Biologists. All rights reserved.

De plantis vascularibus praesertim ibericis (IV

Directory of Open Access Journals (Sweden)

PEDROL, J., YERA, J., ASCASO, J.

2002-01-01

Full Text Available Se aportan algunas novedades florísticas y comentarios corológicos relativos a la zona central del Valle del Ebro (Huesca, Lérida y Zaragoza en España. Destacamos : Achillea filipendulina, Aegilops neglecta, Bbidens aurea, B. fondosa, Centaurea depressa, Chamaemelum nobile, Crypsis aculeata, Cyperus michelianus subsp. michelianus, C. serotinus, Heteranthera reniformis, Mantisalca duriaei, Pulicaria paludosa, Ranunculus sardous, Reichardia intermedia, Scirpus lacustris subsp. lacustris, S. mucronatus, S. supinus, seneciio lagascanus, Sonchus x novocastellanus y Valerianella eriocarpa.

The challenge that Confucian filial piety poses for Korean churches

Directory of Open Access Journals (Sweden)

David M. Park

2014-04-01

Full Text Available Contemporary ancestor worship is currently practiced around the world in several different forms. However, the essence and practice of ancestor worship varies throughout Asia, Africa, Oceania and Latin America. The context of countries under the influence of Confucianism is very different from that of other countries. Confucianism teaches that ancestor worship is the most prized display of filial piety toward one’s dead ancestors. Amongst Asian countries under the influence of Confucianism – specifically China, Japan, Malaysia, Taiwan, Vietnam and Korea – ancestor worship has not only been accepted and propagated as a culture, but it is also considered to be filial piety. Especially the Korean people think that ancestor worship is a very important expression of filial piety, and it is a ritual which they practice regularly during their festive days. What does Confucianism teach about filial piety, and how is ancestor worship practiced? What does the Bible teach about filial piety? Are practical applications of biblical filial piety present in Korean society? Rather than allowing Confucian ancestor worship to take root in Korean society as a traditional Korean heritage, the conclusion is that Korean Christians must make an effort to teach and facilitate biblical filial piety.

Modeling the genealogy of a cultural trait.

Science.gov (United States)

Aguilar, Elliot; Ghirlanda, Stefano

2015-05-01

The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of individuals, a cultural common ancestor does not necessarily exist. We then introduce a related concept: the most recent unique ancestor (MRUA), i.e., the most recent single individual who is the earliest cultural ancestor of the sample. We show that, under neutral evolution, the time to the MRUA can be staggeringly larger than the time to MRCA in a single ancestor model, except when the average number of learning opportunities per individuals is small. Our results point out that the properties of cultural genealogies may be very different from those of genetic genealogies, with potential implications for reconstructing the histories of cultural traits. Copyright © 2014 Elsevier Inc. All rights reserved.

gious role of ancestors in Nyakyusa belief

African Journals Online (AJOL)

the Nyakyusa religion on Malawi's northern border with Tanzania challenges John. Mbiti's reductionist ... Divinitiy or divinities? .... al rather than in dogma, but dogma is rather implicit than explicit. ... Any attitude to or in connection with the ...

Apparatus Named after Our Academic Ancestors--I

Science.gov (United States)

Greenslade, Thomas B., Jr.

2010-01-01

Let us now praise famous physicists, and the apparatus named after them, with apologies to the writer of Ecclesiastes. I once compiled a list of about 300 pieces of apparatus known to us as X's Apparatus. Some of the values of X are familiar, like Wheatstone and Kelvin and Faraday, but have you heard of Pickering or Rhumkorff or Barlow? In an…

Characterization of a new synthetic wheat – Aegilops biuncialis ...

African Journals Online (AJOL)

STORAGESEVER

2009-07-20

Jul 20, 2009 ... Therefore, it could be concluded that Line 15-3-2 is a new synthetic wheat – A. biuncialis partial amphiploid, and .... races (data not shown). Moreover, its ... ways presented on the distal of short arms (Schneider et al., 2005).

The challenge that Confucian filial piety poses for Korean churches ...

African Journals Online (AJOL)

Journal Home > Vol 70, No 2 (2014) > ... Contemporary ancestor worship is currently practiced around the world in several different forms. However, the essence and practice of ancestor worship varies throughout Asia, Africa, Oceania and ...

L'aptitude au croisement avec le seigle (Secale cereale L.) d'une lignée hexaploïde de Triticum (cv. " Roazon " résultant d'hybridation interspécifique (Gramineae Juss.)

OpenAIRE

STEFANOWSKA , Grazyna; CAUDERON , Yvonne

1983-01-01

La lignée de blé hexaploïde « Roazon », qui possède les caractères d’adaptation du groupe des blés tendres intensifs de l’Europe de l’Ouest, résulte d’hybridations interspécifiques mettant en jeu des génotypes extérieurs à ce groupe, en présence du cytoplasme d’Aegilops ventricosa. Les auteurs montrent que « Roazon» donne facilement des hybrides avec le seigle « Petkus » et discutent de l’origine de cette caractéristique également inhabituelle chez les blés tendres européens....

Phylogenomics and evolution of floral traits in the Neotropical tribe Malmeeae (Annonaceae)

NARCIS (Netherlands)

Lopes, J.C.; Chatrou, L.W.; Mello-Silva, de R.; Rudall, P.J.; Sajo, M.G.

2017-01-01

Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have

Fish based diets cause archaeological dating problems

DEFF Research Database (Denmark)

Philippsen, Bente; Rørbæk, Rasmus

2013-01-01

Every time our ancestors cooked freshwater fish in ceramic vessels, they unwittingly set a Carbon-14 trap for future archaeologists......Every time our ancestors cooked freshwater fish in ceramic vessels, they unwittingly set a Carbon-14 trap for future archaeologists...

Mapping of stripe rust resistance gene in an Aegilops caudata ...

Indian Academy of Sciences (India)

Seedling resistance is usually race-specific, but often pro- vides complete ... Genomic DNA was extracted using the CTAB method of. Saghai-Maroof ... Polymerase chain reactions (PCR) were performed in ..... The continuous supply of the rust ...

Evolution of king crabs from hermit crab ancestors

Science.gov (United States)

Cunningham, C. W.; Blackstone, N. W.; Buss, L. W.

1992-02-01

KING crabs (Family Lithodidae) are among the world's largest arthropods, having a crab-like morphology and a strongly calcified exoskeleton1-6. The hermit crabs, by contrast, have depended on gastropod shells for protection for over 150 million years5,7. Shell-living has constrained the morphological evolution of hermit crabs by requiring a decalcified asymmetrical abdomen capable of coiling into gastropod shells and by preventing crabs from growing past the size of the largest available shells1-6. Whereas reduction in shell-living and acquisition of a crab-like morphology (carcinization) has taken place independently in several hermit crab lineages, and most dramatically in king crabs1-6, the rate at which this process has occurred was entirely unknown2,7. We present molecular evidence that king crabs are not only descended from hermit crabs, but are nested within the hermit crab genus Pagurus. We estimate that loss of the shell-living habit and the complete carcinization of king crabs has taken between 13 and 25 million years.

Developing Multi-Level Institutions from Top-Down Ancestors

Directory of Open Access Journals (Sweden)

Martha Dowsley

2007-11-01

Full Text Available The academic literature contains numerous examples of the failures of both top-down and bottom-up common pool resource management frameworks. Many authors agree that management regimes instead need to utilize a multi-level governance approach to meet diverse objectives in management. However, many currently operating systems do not have that history. This paper explores the conversion of ancestral top-down regimes to complex systems involving multiple scales, levels and objectives through the management of the polar bear (Ursus maritimus in its five range countries. The less successful polar bear management systems continue to struggle with the challenges of developing institutions with the capacity to learn and change, addressing multiple objectives while recognizing the conservation backbone to management, and matching the institutional scale with biophysical, economic and social scales. The comparatively successful institutions incorporate these features, but reveal on-going problems with vertical links that are partially dealt with through the creation of links to other groups.

Contrasting patterns of evolution of 45S and 5S rDNA families uncover new aspects in the genome constitution of the agronomically important grass Thinopyrum intermedium (Triticeae).

Science.gov (United States)

Mahelka, Václav; Kopecky, David; Baum, Bernard R

2013-09-01

We employed sequencing of clones and in situ hybridization (genomic and fluorescent in situ hybridization [GISH and rDNA-FISH]) to characterize both the sequence variation and genomic organization of 45S (herein ITS1-5.8S-ITS2 region) and 5S (5S gene + nontranscribed spacer) ribosomal DNA (rDNA) families in the allohexaploid grass Thinopyrum intermedium. Both rDNA families are organized within several rDNA loci within all three subgenomes of the allohexaploid species. Both families have undergone different patterns of evolution. The 45S rDNA family has evolved in a concerted manner: internal transcribed spacer (ITS) sequences residing within the arrays of two subgenomes out of three got homogenized toward one major ribotype, whereas the third subgenome contained a minor proportion of distinct unhomogenized copies. Homogenization mechanisms such as unequal crossover and/or gene conversion were coupled with the loss of certain 45S rDNA loci. Unlike in the 45S family, the data suggest that neither interlocus homogenization among homeologous chromosomes nor locus loss occurred in 5S rDNA. Consistently with other Triticeae, the 5S rDNA family in intermediate wheatgrass comprised two distinct array types-the long- and short-spacer unit classes. Within the long and short units, we distinguished five and three different types, respectively, likely representing homeologous unit classes donated by putative parental species. Although the major ITS ribotype corresponds in our phylogenetic analysis to the E-genome species, the minor ribotype corresponds to Dasypyrum. 5S sequences suggested the contributions from Pseudoroegneria, Dasypyrum, and Aegilops. The contribution from Aegilops to the intermediate wheatgrass' genome is a new finding with implications in wheat improvement. We discuss rDNA evolution and potential origin of intermediate wheatgrass.

Genome digging: insight into the mitochondrial genome of Homo.

Directory of Open Access Journals (Sweden)

Igor V Ovchinnikov

2010-12-01

Full Text Available A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1 into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2 with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N/d(S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity

Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor.

Directory of Open Access Journals (Sweden)

Nataliya Petryk

Full Text Available The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4, we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H2O2 hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H2O2. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.

Gender Roles Revisited: The Development of the "Woman's Place" among African American Women in the United States.

Science.gov (United States)

Burgess, Norma J.

1994-01-01

Examines the black female's role in U.S. society, particularly with regard to working outside the home, and argues that one cannot understand what African American women are today without having a historical perspective for what their ancestors and their ancestors' roles, functions, and responsibilities were. An Afrocentric perspective is…

Identification of hemiclonal reproduction in three species of Hexagrammos marine reef fishes.

Science.gov (United States)

Kimura-Kawaguchi, M R; Horita, M; Abe, S; Arai, K; Kawata, M; Munehara, H

2014-08-01

Natural hybrids between the boreal species Hexagrammos octogrammus and two temperate species Hexagrammos agrammus and Hexagrammos otakii were observed frequently in southern Hokkaido, Japan. Previous studies revealed that H. octogrammus is a maternal ancestor of both hybrids; the hybrids are all fertile females and they frequently breed with paternal species. Although such rampant hybridization occurs, species boundaries have been maintained in the hybrid zone. Possible explanations for the absence of introgressions, despite the frequent backcrossing, might include clonal reproduction: parthenogenesis, gynogenesis and hybridogenesis. The natural hybrids produced haploid eggs that contained only the H. octogrammus genome (maternal ancestor) with discarded paternal genome and generated F1 -hybrid type offspring by fertilization with the haploid sperm of H. agrammus or H. otakii (paternal ancestor). This reproductive mode was found in an artificial backcross hybrid between the natural hybrid and a male of the paternal ancestor. These findings indicate that the natural hybrids adopt hybridogenesis with high possibility and produce successive generations through hybridogenesis by backcrossing with the paternal ancestor. These hybrids of Hexagrammos represent the first hybridogenetic system found from marine fishes that widely inhabit the North Pacific Ocean. In contrast with other hybridogenetic systems, these Hexagrammos hybrids coexist with all three ancestral species in the hybrid zone. The coexistence mechanism is also discussed. © 2014 The Fisheries Society of the British Isles.

"Left High and Dry": Federal Land Policies and Pima Agriculture, 1860-1910

Science.gov (United States)

Dejong, David H.

2009-01-01

The Akimel O'odham, or "River People" (Pima), have lived in the middle Gila River Valley for centuries, irrigating and cultivating the same land as their Huhugam ancestors did for millennia. Continuing their irrigated agricultural economy bequeathed to them by their Huhugam ancestors, the Pima leveraged a favorable geopolitical setting into a…

25 CFR 75.9 - Application form.

Science.gov (United States)

2010-04-01

... applicant. If the application is filed on behalf of a minor, the name and address of the person filing the application and his relationship to the minor. (b) The name, relationship, tribe and roll number of the ancestor or ancestors through whom enrollment rights are claimed, and whether applicant is enrolled with...

Download this PDF file

African Journals Online (AJOL)

hond

2007-04-07

Apr 7, 2007 ... effects of apartheid among blacks is depicted ebulliently alongside ... will face retribution when his ancestors descend upon him and ask ..... Bloke Modisane's confession to believing in ancestors is significant in two major re- .... that even as he returns home in his old age and is gratified by the way the rural,.

Variations in the presence of chloride cells in the gills of lampreys (Petromyzontiformes) and their evolutionary implications.

Science.gov (United States)

Bartels, H; Docker, M F; Krappe, M; White, M M; Wrede, C; Potter, I C

2015-04-01

Although confined to fresh water, non-parasitic species of lampreys and the landlocked parasitic sea lamprey, all of which were derived relatively recently from an adromous ancestors, still develop chloride cells, whose function in their ancestors was for osmoregulation in marine waters during the adult parasitic phase. In contrast, such cells are not developed by the non-parasitic least brook lamprey Lampetra aepyptera, which has been separated from its ancestor for >2 million years, nor by the freshwater parasitic species of the genus Ichthyomyzon. The length of time that a non-parasitic species or landlocked parasitic form or species has spent in fresh water is thus considered the overriding factor determining whether chloride cells are developed by those lampreys.

Recent advances in forest products research and development

Science.gov (United States)

Joseph E. Jakes

2016-01-01

Wood has always played an integral role in meeting our materials needs. The earliest evidence of woodworking dates back 1.5 million years to the modern human ancestor Homo erectus.1 Many characteristics that made wood a favorable material for our ancestors—relative abundance, ease of forming and shaping, exceptional strength-toweight ratio,...

Introgression of a leaf rust resistance gene from Aegilops caudata to ...

Indian Academy of Sciences (India)

tance genes (Lr) and 48 stripe rust resistance genes (Yr) have .... Leaf rust reaction of the parents, wheat – Ae. caudata introgression lines and representative F2 plants developed from the cross: .... segregation ratio, which is otherwise a serious problem with ... Financial assistance was provided by the USDA-ARS under the.

Mortal Ancestors, Immortal Images: Zhang Dai’s Biographical Portraits

Directory of Open Access Journals (Sweden)

Duncan M. Campbell

2012-11-01

Full Text Available Towards the end of his long life, the prolific late-Ming historian and essayist Zhang Dai 張岱 (1597-?1684 completed a book that he had been working on for many years. Entitled Portraits of the Eminent and Worthy Immortals of Zhejiang During the Ming Dynasty (You Ming yuyue san bu xiu tuzan 有明於越三不朽名賢圖贊 the book included the short biographies (with poetic panegyrics and portraits of 109 men and women of Zhang Dai’s hometown of Shaoxing, one of the epicentres of China’s élite cultural life. The book was organised according to the “Three Immortalities of Life”: moral force, meritorious service, and wise words. Zhang also included a number of his own friends and family members in this collection. This paper discusses aspects the relationship between text and image in this late-imperial Chinese work, both in the context of Zhang Dai’s practice as a biographer who had a strong visual sense and in regard to his particular historical plight as someone who had survived the collapse of one dynasty and who had lived on under its successor regime.

Mortal Ancestors, Immortal Images: Zhang Dai’s Biographical Portraits

OpenAIRE

Duncan M. Campbell

2012-01-01

Towards the end of his long life, the prolific late-Ming historian and essayist Zhang Dai 張岱 (1597-?1684) completed a book that he had been working on for many years. Entitled Portraits of the Eminent and Worthy Immortals of Zhejiang During the Ming Dynasty (You Ming yuyue san bu xiu tuzan 有明於越三不朽名賢圖贊) the book included the short biographies (with poetic panegyrics) and portraits of 109 men and women of Zhang Dai’s hometown of Shaoxing, one of the epicentres of China’s élite cultural life. Th...

What Our Ancestors Knew: Teaching and Learning through Storytelling

Science.gov (United States)

Lawrence, Randee Lipson; Paige, Dennis Swiftdeer

2016-01-01

The art of storytelling is traced from its roots in indigenous cultural societies. Storytelling in education is described as a participatory learning process that promotes community and understanding.

Deconstructing Jaco: genetic heritage of an Afrikaner.

Science.gov (United States)

Greeff, J M

2007-09-01

It is often assumed that Afrikaners stem from a small number of Dutch immigrants. As a result they should be genetically homogeneous, show founder effects and be rather inbred. By disentangling my own South African pedigree, that is on average 12 generations deep, I try to quantify the genetic heritage of an Afrikaner. As much as 6% of my genes have been contributed by slaves from Africa, Madagascar and India, and a woman from China. This figure compares well to other genetic and genealogical estimates. Seventy three percent of my lineages coalesce into common founders, and I am related in excess of 10 times to 20 founder ancestors (30 times to Willem Schalk van der Merwe). Significant founder effects are thus possible. The overrepresentation of certain founder ancestors is in part explained by the fact that they had more children. This is remarkable given that they lived more than 300 years (or 12 generations) ago. DECONSTRUCT, a new program for pedigree analysis, identified 125 common ancestors in my pedigree. However, these common ancestors are so distant from myself, paths of between 16 and 25 steps in length, that my inbreeding coefficient is not unusually high (f approximately 0.0019).

Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach

Institute of Scientific and Technical Information of China (English)

AJ HARRIS; Jun WEN; Qiu-Yun (Jenny) XIANG

2013-01-01

The arcto-Tertiary relictual flora is comprised of many genera that occur non-contiguously in the temperate zones of eastern Asia,Europe,eastern North America,and westem North America.Within each distributional area,species are typically endemic and may thus be widely separated from closely related species within the other areas.It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once morecontinuous arcto-Tertiary forest.The historical biogeographic events leading to the present-day disjunction have often been investigated using a phylogenetic approach.Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions.However,the recently described Bayes-DIVA method handles both types of uncertainty.Thus,we used Bayes-DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families.In particular,we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors,(2) ancestors dispersed from other areas,or (3) endemic ancestors.We also considered which of these three biogeographic mechanisms may best explain the origins of arcto-Tertiary disjunct endemics in the neotropics.Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America.Present-day endemic lineages in the latter areas more often arose from widespread ancestors.Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto-Tertiary species endemic in the neotropics.

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage.

OpenAIRE

Bonito, Gregory; Smith, Matthew E.; Nowak, Michael; Healy, Rosanne A.; Guevara, Gonzalo; Cázares, Efren; Kinoshita, Akihiko; Nouhra, Eduardo Ramon; Dominguez, Laura Susana; Tedersoo, Leho; Murat, Claude; Wang, Yun; Arroyo Moreno, Baldomero; Pfister, Donald H.; Nara, Kazuhide

2015-01-01

Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses ...

Hunter-Gatherers and the Origins of Religion.

Science.gov (United States)

Peoples, Hervey C; Duda, Pavel; Marlowe, Frank W

2016-09-01

Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

Science.gov (United States)

Sunobe, Tomoki; Sado, Tetsuya; Hagiwara, Kiyoshi; Manabe, Hisaya; Suzuki, Toshiyuki; Kobayashi, Yasuhisa; Sakurai, Makoto; Dewa, Shin-ichi; Matsuoka, Midori; Shinomiya, Akihiko; Fukuda, Kazuya; Miya, Masaki

2017-04-01

Size-advantage and low-density models have been used to explain how mating systems favor hermaphroditism or gonochorism. However, these models do not indicate historical transitions in sexuality. Here, we investigate the evolution of bidirectional sex change and gonochorism by phylogenetic analysis using the mitochondrial gene of the gobiids Trimma (31 species), Priolepis (eight species), and Trimmatom (two species). Trimma and Priolepis formed a clade within the sister group Trimmatom. Gonadal histology and rearing experiments revealed that Trimma marinae, Trimma nasa, and Trimmatom spp. were gonochoric, whereas all other Trimma and Priolepis spp. were bidirectional sex changers or inferred ones. A maximum-likelihood reconstruction analysis demonstrated that the common ancestor of the three genera was gonochoristic. Bidirectional sex change probably evolved from gonochorism in a common ancestor of Trimma and Priolepis. As the gonads of bidirectional sex changers simultaneously contain mature ovarian and immature testicular components or vice versa, individuals are always potentially capable of functioning as females or males, respectively. Monogamy under low-density conditions may have been the ecological condition for the evolution of bidirectional sex change in a common ancestor. As T. marinae and T. nasa are a monophyletic group, gonochorism should have evolved from bidirectional sex change in a common ancestor.

[Genetic aspects of genealogy].

Science.gov (United States)

Tetushkin, E Iu

2011-11-01

The supplementary historical discipline genealogy is also a supplementary genetic discipline. In its formation, genetics borrowed from genealogy some methods of pedigree analysis. In the 21th century, it started receiving contribution from computer-aided genealogy and genetic (molecular) genealogy. The former provides novel tools for genetics, while the latter, which employing genetic methods, enriches genetics with new evidence. Genealogists formulated three main laws ofgenealogy: the law of three generations, the law of doubling the ancestry number, and the law of declining ancestry. The significance and meaning of these laws can be fully understood only in light of genetics. For instance, a controversy between the exponential growth of the number of ancestors of an individual, i.e., the law of doubling the ancestry number, and the limited number of the humankind is explained by the presence of weak inbreeding because of sibs' interference; the latter causes the pedigrees' collapse, i.e., explains also the law of diminishing ancestry number. Mathematic modeling of pedigrees' collapse presented in a number of studies showed that the number of ancestors of each individual attains maximum in a particular generation termed ancestry saturated generation. All representatives of this and preceding generation that left progeny are common ancestors of all current members of the population. In subdivided populations, these generations are more ancient than in panmictic ones, whereas in small isolates and social strata with limited numbers of partners, they are younger. The genealogical law of three generations, according to which each hundred years contain on average three generation intervals, holds for generation lengths for Y-chromosomal DNA, typically equal to 31-32 years; for autosomal and mtDNA, this time is somewhat shorter. Moving along ascending lineas, the number of genetically effective ancestors transmitting their DNA fragment to descendants increases far

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Directory of Open Access Journals (Sweden)

Galperin Michael Y

2003-01-01

Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties

How to Grow Old

Institute of Scientific and Technical Information of China (English)

Bertrand Russell

2008-01-01

<正>1. In spite of the title, this article will really be on how not to grow old, which, at my time of life, is a much more important subject. My first advice would be to choose your ancestors carefully. Although both my parents died young, I have done well in this respect as regards my other ancestors. My maternal grandfather, it is true, was cut off in the flower of his youth at the age of sixty-seven,

Experimental induction of struvite uroliths in miniature schnauzer and beagle dogs.

Science.gov (United States)

Klausner, J S; Osborne, C A; O'Leary, T P; Muscoplat, C M; Griffith, D P

1980-09-01

Urease positive staphylococcal urinary tract infection was experimentally induced in 13 dogs. Eight dogs developed cystic and/or urethral struvite calculi in 2 to 8 weeks. No abnormalities in systemic cell mediated immunity were detected in dogs before or after the establishment of the urinary tract infection. Miniature schnauzers whose ancestors had developed stones seemed to be no more susceptible to experimental urinary tract infection and stone formation than miniature schnauzers or beagles whose ancestors did not develop stones.

ORF Alignment: NC_005945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005945 gi|49185498 >1kwfA 3 362 53 435 1e-84 ... ref|YP_019314.1| chitosanase [Bac...illus anthracis str. 'Ames Ancestor'] ... ref|NP_845032.1| chitosanase [Bacillus anthracis str. ... ... ... Ames] ref|YP_028750.1| chitosanase [Bacillus anthracis ... str. Sterne] ref|NP_656550.1| Glyco_... ... gb|AAP26518.1| chitosanase [Bacillus anthracis str. ... Ames] gb|AAT31789.1| chitosanase [...Bacillus anthracis ... str. 'Ames Ancestor'] gb|AAT54801.1| chitosanase ... [Bacillus anthraci

ORF Alignment: NC_003995 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003995 gi|21400565 >1kwfA 3 362 53 435 1e-84 ... ref|YP_019314.1| chitosanase [Bac...illus anthracis str. 'Ames Ancestor'] ... ref|NP_845032.1| chitosanase [Bacillus anthracis str. ... ... ... Ames] ref|YP_028750.1| chitosanase [Bacillus anthracis ... str. Sterne] ref|NP_656550.1| Glyco_... ... gb|AAP26518.1| chitosanase [Bacillus anthracis str. ... Ames] gb|AAT31789.1| chitosanase [...Bacillus anthracis ... str. 'Ames Ancestor'] gb|AAT54801.1| chitosanase ... [Bacillus anthraci

ORF Alignment: NC_003997 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003997 gi|30262655 >1kwfA 3 362 53 435 1e-84 ... ref|YP_019314.1| chitosanase [Bac...illus anthracis str. 'Ames Ancestor'] ... ref|NP_845032.1| chitosanase [Bacillus anthracis str. ... ... ... Ames] ref|YP_028750.1| chitosanase [Bacillus anthracis ... str. Sterne] ref|NP_656550.1| Glyco_... ... gb|AAP26518.1| chitosanase [Bacillus anthracis str. ... Ames] gb|AAT31789.1| chitosanase [...Bacillus anthracis ... str. 'Ames Ancestor'] gb|AAT54801.1| chitosanase ... [Bacillus anthraci

ORF Alignment: NC_007530 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_007530 gi|47527965 >1kwfA 3 362 53 435 1e-84 ... ref|YP_019314.1| chitosanase [Bac...illus anthracis str. 'Ames Ancestor'] ... ref|NP_845032.1| chitosanase [Bacillus anthracis str. ... ... ... Ames] ref|YP_028750.1| chitosanase [Bacillus anthracis ... str. Sterne] ref|NP_656550.1| Glyco_... ... gb|AAP26518.1| chitosanase [Bacillus anthracis str. ... Ames] gb|AAT31789.1| chitosanase [...Bacillus anthracis ... str. 'Ames Ancestor'] gb|AAT54801.1| chitosanase ... [Bacillus anthraci

Reconstruction of ancestral RNA sequences under multiple structural constraints

OpenAIRE

Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

2016-01-01

Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

British Museum Exhibition Review: The Jericho Skull, Creating an Ancestor

Directory of Open Access Journals (Sweden)

Cara Hirst

2017-03-01

Full Text Available The temporary exhibit at the British Museum, open 15th December-19th February, and located to the right of the main entrance in the Raymond and Beverly Sackler Gallery (Room 59; is dedicated to a single Neolithic crania from Jericho, known as the Jericho Skull. This exhibit demonstrates the value of relatively recent technologies in archaeological research, highlighting the previously hidden information made possible through CT scanning and the value of these methods in both archaeological research but also in communicating archaeology in a visually stimulating manner which allows an exhibit to take a single item, and create an in depth exhibit featuring both the original material and two cranial 3D prints along with a facial reconstruction.

Health and Ancestors: The Case of South Africa and Beyond

African Journals Online (AJOL)

denise

The IPJP is a joint project of the Humanities Faculty of the University of Johannesburg (South Africa) and Edith Cowan ... This work is licensed to the publisher under the Creative Commons Attributions License 3.0 .... that can be successful without the guidance and co- .... the failure by the family to perform a certain ritual.

Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize

Science.gov (United States)

Fang, Zhou; Pyhäjärvi, Tanja; Weber, Allison L.; Dawe, R. Kelly; Glaubitz, Jeffrey C.; González, José de Jesus Sánchez; Ross-Ibarra, Claudia; Doebley, John; Morrell, Peter L.; Ross-Ibarra, Jeffrey

2012-01-01

Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ∼50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures >700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles. PMID:22542971

Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes.

Science.gov (United States)

Zheng, Chunfang; Zhu, Qian; Adam, Zaky; Sankoff, David

2008-07-01

Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to 'halve' the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly nonunique. To resolve this problem, we take account of outgroups, external reference genomes, to guide and narrow down the search. We improve on a previous, computationally costly, 'brute force' method by adapting the genome halving algorithm of El-Mabrouk and Sankoff so that it rapidly and accurately constructs an ancestor close the outgroups, prior to a local optimization heuristic. We apply this to reconstruct the predoubling ancestor of Saccharomyces cerevisiae and Candida glabrata, guided by the genomes of three other yeasts that diverged before the genome doubling event. We analyze the results in terms (1) of the minimum evolution criterion, (2) how close the genome halving result is to the final (local) minimum and (3) how close the final result is to an ancestor manually constructed by an expert with access to additional information. We also visualize the set of reconstructed ancestors using classic multidimensional scaling to see what aspects of the two doubled and three unduplicated genomes influence the differences among the reconstructions. The experimental software is available on request.

Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes.

Science.gov (United States)

Rhee, Je-Keun; Kim, Tae-Min

2018-04-20

It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown. In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types. As a result, we identified tumor type-specific directed networks composed of 2-15 cancer-related genes (nodes) and their mutational orders (edges). The most common ancestors identified in pairwise comparison of somatic mutations were TP53 mutations in breast, head/neck, and lung cancers. The known relationship of KRAS to TP53 mutations in colorectal cancers was identified, as well as potential ancestors of TP53 mutation such as NOTCH1, EGFR, and PTEN mutations in head/neck, lung and endometrial cancers, respectively. We also identified apoptosis-related genes enriched with ancestor mutations in lung cancers and a relationship between APC hotspot mutations and TP53 mutations in colorectal cancers. While evolutionary analysis of cancers has focused on clonal versus subclonal mutations identified in individual genomes, our analysis aims to further discriminate ancestor versus descendant mutations in population-scale mutation profiles that may help select cancer drivers with clinical relevance.

ORF Alignment: NC_007530 [GENIUS II[Archive

Lifescience Database Archive (English)

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GAMBARAN KEPERCAYAAN TENTANG KHASIAT MENYIRIH PADA MASYARAKAT PAPUA DI KELURAHAN ARDIPURA I DISTRIK JAYAPURA SELATAN KOTA JAYAPURA

OpenAIRE

Kamisorei, Rahel Violin; Devy, Shrimarti Rukmini

2018-01-01

Indonesian people has long know the, betel leaf, areca nut, and lime is material to betel chewing. Chewing the betel leaf is believed can care teeth by ancestors. They are convinced that slacking can strengthen teeth, cure small cuts in the mouth, eliminate bad breath. Indigenous Papuans engage in slaughtering behavior because of the belief inherited from the ancestors. The frequency of betel chewing practiced by indigenous people of Papua is > 2 times a day by consuming more than two areca n...

Gametocidal chromosomes enhancing chromosome aberration in common wheat induced by 5-azacytidine.

Science.gov (United States)

Su, W-Y; Cong, W-W; Shu, Y-J; Wang, D; Xu, G-H; Guo, C-H

2013-07-08

The gametocidal (Gc) chromosome from Aegilops spp induces chromosome mutation, which is introduced into common wheat as a tool of chromosome manipulation for genetic improvement. The Gc chromosome functions similar to a restriction-modification system in bacteria, in which DNA methylation is an important regulator. We treated root tips of wheat carrying Gc chromosomes with the hypomethylation agent 5-azacytidine; chromosome breakage and micronuclei were observed in these root tips. The frequency of aberrations differed in wheat containing different Gc chromosomes, suggesting different functions inducing chromosome breakage. Gc chromosome 3C caused the greatest degree of chromosome aberration, while Gc chromosome 3C(SAT) and 2C caused only slight chromosome aberration. Gc chromosome 3C induced different degrees of chromosome aberration in wheat varieties Triticum aestivum var. Chinese Spring and Norin 26, demonstrating an inhibition function in common wheat.

'They Say HIV is a Punishment from God or from Ancestors': Cross-Cultural Adaptation and Psychometric Assessment of an HIV Stigma Scale for South African Adolescents Living with HIV (ALHIV-SS).

Science.gov (United States)

Pantelic, Marija; Boyes, Mark; Cluver, Lucie; Thabeng, Mildred

2018-01-01

Sub-Saharan Africa is home to 90 % of the world's adolescents living with HIV (ALHIV). HIV-stigma and the resultant fear of being identified as HIV-positive can compromise the survival of these youth by undermining anti-retroviral treatment initiation and adherence. To date, no HIV-stigma measures have been validated for use with ALHIV in Sub-Saharan Africa. This paper reports on a two-stage study in the Eastern Cape, South Africa. Firstly, we conducted a cross-cultural adaptation of an HIV stigma scale, previously used with US ALHIV. One-on-one semi-structured cognitive interviews were conducted with 9 urban and rural ALHIV. Three main themes emerged: 1) participants spoke about experiences of HIV stigma specific to a Southern African context, such as anticipating stigma from community members due to 'punishment from God or ancestors'; 2) participants' responses uncovered discrepancies between what the items intended to capture and how they understood them and 3) participants' interpretation of wording uncovered redundant items. Items were revised or removed in consultation with participants. Secondly, we psychometrically assessed and validated this adapted ALHIV stigma scale (ALHIV-SS). We used total population sampling in 53 public healthcare facilities with community tracing. 721 ALHIV who were fully aware of their status were identified and interviewed for the psychometric assessment. Confirmatory factor analysis confirmed a 3-factor structure of enacted, anticipated and internalized stigma. The removal of 3 items resulted in a significant improvement in model fit ( Chi 2 (df)  = 189.83 (33), p  < .001) and the restricted model fitted the data well (RMSEA = .017; CFI/TLI = .985/.980; SRMR = .032). Standardized factor loadings of indicators onto the latent variable were acceptable for all three measures (.41-.96). Concurrent criterion validity confirmed hypothesized relationships. Enacted stigma was associated with higher AIDS

GRtoGR: a system for mapping GO relations to gene relations.

Science.gov (United States)

Taha, Kamal

2013-12-01

We introduce in this paper a biological search engine called GRtoGR. Given a set of S genes, GRtoGR would determine from GO graph the most significant Lowest Common Ancestor (LCA) of the GO terms annotating the set S. This significant LCA annotates the genes that are the most semantically related to the set S. The framework of GRtoGR refines the concept of LCA by introducing the concepts of Relevant Lowest Common Ancestor (RLCA) and Semantically Relevant Lowest Common Ancestor (SRLCA). A SRLCA is the most significant LCA of the GO terms annotating the set S. We observe that the existence of the GO terms annotating the set S is dependent on the existence of this SRLCA in GO graph. That is, the terms annotating a given set of genes usually have existence dependency relationships with the SRLCA of these terms. We evaluated GRtoGR experimentally and compared it with nine other methods. Results showed marked improvement.

ORF Sequence: NC_007530 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available [Bacillus anthracis str. 'Ames Ancestor'] MSNNNYSNGLNPDESLSASAFDPNLVGPTLPPIPPFTLPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGDTGTTGPTGPTGPTGPTGP...TGDTGTTGPTGPTGPTGPTGPTGPTGPTGDTGTTGPTGPTGPTGPTGPTGDTGTTGPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGPTGDTGTTGPTGPTGP...TGPTGPTGDTGTTGPTGPTGPTGPTGPTGPTGPTGATGLTGPTGPTGPSGLGLPAGL

ORF Alignment: NC_003995 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003995 gi|21402596 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_005945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005945 gi|49187443 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_003997 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003997 gi|30264621 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

Positively selected sites in cetacean myoglobins contribute to protein stability

DEFF Research Database (Denmark)

Dasmeh, Pouria; Serohijos, Adrian W R; Kepp, Kasper P

2013-01-01

Since divergence ∼50 Ma ago from their terrestrial ancestors, cetaceans underwent a series of adaptations such as a ∼10-20 fold increase in myoglobin (Mb) concentration in skeletal muscle, critical for increasing oxygen storage capacity and prolonging dive time. Whereas the O2-binding affinity...... between Mb folding stability and protein abundance, suggesting that a selection pressure for stability acts proportionally to higher expression. We also identify a major divergence event leading to the common ancestor of whales, during which major stabilization occurred. Most of the positively selected...

Working Memory: A Cognitive Limit to Non-Human Primate Recursive Thinking Prior to Hominid Evolution

Directory of Open Access Journals (Sweden)

Dwight W. Read

2008-10-01

Full Text Available In this paper I explore the possibility that recursion is not part of the cognitive repertoire of non-human primates such as chimpanzees due to limited working memory capacity. Multiple lines of data, from nut cracking to the velocity and duration of cognitive development, imply that chimpanzees have a short-term memory size that limits working memory to dealing with two, or at most three, concepts at a time. If so, as a species they lack the cognitive capacity for recursive thinking to be integrated into systems of social organization and communication. If this limited working memory capacity is projected back to a common ancestor for Pan and Homo, it follows that early hominid ancestors would have had limited working memory capacity. Hence we should find evidence for expansion of working memory capacity during hominid evolution reflected in changes in the products of conceptually framed activities such as stone tool production. Data on the artifacts made by our hominid ancestors support this expansion hypothesis for hominid working memory, thereby leading to qualitative differences between Pan and Homo.

Did the ancient Egyptians migrate to ancient Nigeria?

Directory of Open Access Journals (Sweden)

Jock M. Agai

2014-01-01

Full Text Available Literatures concerning the history of West African peoples published from 1900 to 1970 debate�the possible migrations of the Egyptians into West Africa. Writers like Samuel Johnson and�Lucas Olumide believe that the ancient Egyptians penetrated through ancient Nigeria but Leo�Frobenius and Geoffrey Parrinder frowned at this opinion. Using the works of these early�20th century writers of West African history together with a Yoruba legend which teaches�about the origin of their earliest ancestor(s, this researcher investigates the theories that the�ancient Egyptians had contact with the ancient Nigerians and particularly with the Yorubas.Intradisciplinary and/or interdisciplinary implications: There is an existing ideology�amongst the Yorubas and other writers of Yoruba history that the original ancestors of�the Yorubas originated in ancient Egypt hence there was migration between Egypt and�Yorubaland. This researcher contends that even if there was migration between Egypt and�Nigeria, such migration did not take place during the predynastic and dynastic period as�speculated by some scholars. The subject is open for further research.

Fibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis

Directory of Open Access Journals (Sweden)

Fernando Segade

2016-08-01

Full Text Available Abstract Background Genomic analysis has upended chordate phylogeny, placing the tunicates as the sister group to the vertebrates. This taxonomic rearrangement raises questions about the emergence of a tunicate/vertebrate ancestor. Results Characterization of developmental genes uniquely shared by tunicates and vertebrates is one promising approach for deciphering developmental shifts underlying acquisition of novel, ancestral traits. The matrix glycoprotein Fibronectin (FN has long been considered a vertebrate-specific gene, playing a major instructive role in vertebrate embryonic development. However, the recent computational prediction of an orthologous “vertebrate-like” Fn gene in the genome of a tunicate, Ciona savignyi, challenges this viewpoint suggesting that Fn may have arisen in the shared tunicate/vertebrate ancestor. Here we verify the presence of a tunicate Fn ortholog. Transgenic reporter analysis was used to characterize a Ciona Fn enhancer driving expression in the notochord. Targeted knockdown in the notochord lineage indicates that FN is required for proper convergent extension. Conclusions These findings suggest that acquisition of Fn was associated with altered notochord morphogenesis in the vertebrate/tunicate ancestor.

Annelids in evolutionary developmental biology and comparative genomics

Directory of Open Access Journals (Sweden)

Mcdougall C.

2008-09-01

Full Text Available Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

KAUST Repository

Refregier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cö mert, Fü sun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; Mcnerney, Ruth; Pain, Arnab; Clark, Taane G.; Sola, Christophe

2016-01-01

Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.

A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages

NARCIS (Netherlands)

Gueidan, C.; Ruibal Villaseñor, C.; de Hoog, G.S.; Gorbushina, A.A.; Untereiner, W.A.; Lutzoni, F.

2008-01-01

Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare

Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.

Science.gov (United States)

Degnan, Patrick H; Yu, Yeisoo; Sisneros, Nicholas; Wing, Rod A; Moran, Nancy A

2009-06-02

Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria. Hamiltonella defensa, an endosymbiont of aphids and other sap-feeding insects, protects its aphid host from attack by parasitoid wasps. Thus H. defensa is only conditionally beneficial to hosts, unlike ancient nutritional symbionts, such as Buchnera, that are obligate. Similar to pathogenic bacteria, H. defensa is able to invade naive hosts and circumvent host immune responses. We have sequenced the genome of H. defensa to identify possible mechanisms that underlie its persistence in healthy aphids and protection from parasitoids. The 2.1-Mb genome has undergone significant reduction in size relative to its closest free-living relatives, which include Yersinia and Serratia species (4.6-5.4 Mb). Auxotrophic for 8 of the 10 essential amino acids, H. defensa is reliant upon the essential amino acids produced by Buchnera. Despite these losses, the H. defensa genome retains more genes and pathways for a variety of cell structures and processes than do obligate symbionts, such as Buchnera. Furthermore, putative pathogenicity loci, encoding type-3 secretion systems, and toxin homologs, which are absent in obligate symbionts, are abundant in the H. defensa genome, as are regulatory genes that likely control the timing of their expression. The genome is also littered with mobile DNA, including phage-derived genes, plasmids, and insertion-sequence elements, highlighting its dynamic nature and the continued role horizontal gene transfer plays in shaping it.

The Long Evolutionary Journey of Cancer from Ancestor to Modern Humans.

Science.gov (United States)

Carruba, Giuseppe; Trosko, James E

2017-01-01

In this article, we review various key issues in cancer development and progression that have important implications for both cancer prevention and treatment: (1) evolutionary aspects of cancer appearance; (2) evidence of organ-specific adult stem cells as cancer-initiating cells; (3) the immortality of cancer-initiating cells; (4) cancer cell loss of growth control, contact inhibition, terminal differentiation, and apoptosis; (5) stem-cell versus de-differentiation theory of carcinogenesis; (6) mutations in cancer; (7) oncogenes and tumor suppressor genes; (8) epigenetics as the rate-limiting step in carcinogenesis; (9) the potential role of cultural, lifestyle, and nutritional behaviors in oncology; and (10) changes of commensal microbial community and its metagenome in carcinogenesis and tumor progression. Relevant, combined evidence is discussed from a standpoint whereby cancer is considered a multifaceted disease requiring integrated biomolecular and clinico-pathological information to design and implement strategies for either primary prevention or therapy.

"My Ancestors Didn't Own Slaves": Understanding White Talk about Race

Science.gov (United States)

Trainor, Jennifer Seibel

2005-01-01

In this essay, I address the problem of White racism in the classroom, proposing a way of reading racist discourse that takes into account its emotional dimensions and hence its persuasive appeal for White students. This way of reading begins with the insight that racist language functions metaphorically, and that it acts as a rhetorical bridge…

Clawed forelimbs allow northern seals to eat like their ancient ancestors

Science.gov (United States)

Hocking, David P.; Marx, Felix G.; Sattler, Renae; Harris, Robert N.; Pollock, Tahlia I.; Sorrell, Karina J.; Fitzgerald, Erich M. G.; McCurry, Matthew R.; Evans, Alistair R.

2018-04-01

Streamlined flippers are often considered the defining feature of seals and sea lions, whose very name `pinniped' comes from the Latin pinna and pedis, meaning `fin-footed'. Yet not all pinniped limbs are alike. Whereas otariids (fur seals and sea lions) possess stiff streamlined forelimb flippers, phocine seals (northern true seals) have retained a webbed yet mobile paw bearing sharp claws. Here, we show that captive and wild phocines routinely use these claws to secure prey during processing, enabling seals to tear large fish by stretching them between their teeth and forelimbs. `Hold and tear' processing relies on the primitive forelimb anatomy displayed by phocines, which is also found in the early fossil pinniped Enaliarctos. Phocine forelimb anatomy and behaviour therefore provide a glimpse into how the earliest seals likely fed, and indicate what behaviours may have assisted pinnipeds along their journey from terrestrial to aquatic feeding.

Mechanism of photoprotection in the cyanobacterial ancestor of plant antenna proteins

Czech Academy of Sciences Publication Activity Database

Staleva, H.; Komenda, Josef; Shukla, Mahendra K.; Šlouf, V.; Kaňa, Radek; Polívka, Tomáš; Sobotka, Roman

2015-01-01

Roč. 11, č. 4 (2015), s. 287-291 ISSN 1552-4450 R&D Projects: GA ČR GBP501/12/G055; GA ČR(CZ) GA14-13967S; GA MŠk ED2.1.00/03.0110 Institutional support: RVO:61388971 ; RVO:60077344 Keywords : photosystem II * fluorescence * chlorophyll Subject RIV: BO - Biophysics; BO - Biophysics (BC-A) Impact factor: 12.709, year: 2015

Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors

International Nuclear Information System (INIS)

Davies, P C W; Lineweaver, C H

2011-01-01

The genes of cellular cooperation that evolved with multicellularity about a billion years ago are the same genes that malfunction to cause cancer. We hypothesize that cancer is an atavistic condition that occurs when genetic or epigenetic malfunction unlocks an ancient 'toolkit' of pre-existing adaptations, re-establishing the dominance of an earlier layer of genes that controlled loose-knit colonies of only partially differentiated cells, similar to tumors. The existence of such a toolkit implies that the progress of the neoplasm in the host organism differs distinctively from normal Darwinian evolution. Comparative genomics and the phylogeny of basal metazoans, opisthokonta and basal multicellular eukaryotes should help identify the relevant genes and yield the order in which they evolved. This order will be a rough guide to the reverse order in which cancer develops, as mutations disrupt the genes of cellular cooperation. Our proposal is consistent with current understanding of cancer and explains the paradoxical rapidity with which cancer acquires a suite of mutually-supportive complex abilities. Finally we make several predictions and suggest ways to test this model

Evolution of the fish rhabdovirus viral haemorrhagic septicaemia virus

DEFF Research Database (Denmark)

Einer-Jensen, Katja; Ahrens, Peter; Forsberg, Roald

2004-01-01

of free-living marine fish species. To study the genetic evolution of VHSV, the entire G gene from 74 isolates was analysed. VHSV from wild marine species caught in the Baltic Sea, Skagerrak, Kattegat, North Sea, and English Channel and European freshwater isolates, appeared to share a recent common...... ancestor. Based on the estimated nucleotide substitution rate, the ancestor of the European fresh water isolates was dated some 50 years ago. This finding fits with the initial reports in the 1950s on clinical observations of VHS in Danish freshwater rainbow trout farms. The study also indicates...

Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea.

Science.gov (United States)

Groussin, Mathieu; Gouy, Manolo

2011-09-01

Methods to infer the ancestral conditions of life are commonly based on geological and paleontological analyses. Recently, several studies used genome sequences to gain information about past ecological conditions taking advantage of the property that the G+C and amino acid contents of bacterial and archaeal ribosomal DNA genes and proteins, respectively, are strongly influenced by the environmental temperature. The adaptation to optimal growth temperature (OGT) since the Last Universal Common Ancestor (LUCA) over the universal tree of life was examined, and it was concluded that LUCA was likely to have been a mesophilic organism and that a parallel adaptation to high temperature occurred independently along the two lineages leading to the ancestors of Bacteria on one side and of Archaea and Eukarya on the other side. Here, we focus on Archaea to gain a precise view of the adaptation to OGT over time in this domain. It has been often proposed on the basis of indirect evidence that the last archaeal common ancestor was a hyperthermophilic organism. Moreover, many results showed the influence of environmental temperature on the evolutionary dynamics of archaeal genomes: Thermophilic organisms generally display lower evolutionary rates than mesophiles. However, to our knowledge, no study tried to explain the differences of evolutionary rates for the entire archaeal domain and to investigate the evolution of substitution rates over time. A comprehensive archaeal phylogeny and a non homogeneous model of the molecular evolutionary process allowed us to estimate ancestral base and amino acid compositions and OGTs at each internal node of the archaeal phylogenetic tree. The last archaeal common ancestor is predicted to have been hyperthermophilic and adaptations to cooler environments can be observed for extant mesophilic species. Furthermore, mesophilic species present both long branches and high variation of nucleotide and amino acid compositions since the last archaeal

The environmental context of human evolutionary history in Eurasia and Africa.

Science.gov (United States)

Elton, Sarah

2008-04-01

This review has three main aims: (1) to make specific predictions about the habitat of the hypothetical last common ancestor of the chimpanzee/bonobo-human clade; (2) to outline the major trends in environments between 8-6 Ma and the late Pleistocene; and (3) to pinpoint when, and in some cases where, human ancestors evolved to cope with the wide range of habitats they presently tolerate. Several lines of evidence indicate that arboreal environments, particularly woodlands, were important habitats for late Miocene hominids and hominins, and therefore possibly for the last common ancestor of the chimpanzee/bonobo-human clade. However, as there is no clear candidate for this last common ancestor, and because the sampling of fossils and past environments is inevitably patchy, this prediction remains a working hypothesis at best. Nonetheless, as a primate, it is expected that the last common ancestor was ecologically dependent on trees in some form. Understanding past environments is important, as palaeoenvironmental reconstructions provide the context for human morphological and behavioural evolution. Indeed, the impact of climate on the evolutionary history of our species has long been debated. Since the mid-Miocene, the Earth has been experiencing a general cooling trend accompanied by aridification, which intensified during the later Pliocene and Pleistocene. Numerous climatic fluctuations, as well as local, regional and continental geography that influenced weather patterns and vegetation, created hominin environments that were dynamic in space and time. Behavioural flexibility and cultural complexity were crucial aspects of hominin expansion into diverse environments during the Pleistocene, but the ability to exploit varied and varying habitats was established much earlier in human evolutionary history. The development of increasingly complex tool technology facilitated re-expansion into tropical forests. These environments are difficult for obligate bipeds to

The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach.

Science.gov (United States)

Harduin-Lepers, Anne; Mollicone, Rosella; Delannoy, Philippe; Oriol, Rafael

2005-08-01

The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication.

Science.gov (United States)

Kimura, Birgitta; Marshall, Fiona B; Chen, Shanyuan; Rosenbom, Sónia; Moehlman, Patricia D; Tuross, Noreen; Sabin, Richard C; Peters, Joris; Barich, Barbara; Yohannes, Hagos; Kebede, Fanuel; Teclai, Redae; Beja-Pereira, Albano; Mulligan, Connie J

2011-01-07

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

Reconstruction of ancestral RNA sequences under multiple structural constraints.

Science.gov (United States)

Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

2016-11-11

Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Inventing Homo gardarensis: prestige, pressure, and human evolution in interwar Scandinavia.

Science.gov (United States)

Kjaergaard, Peter C

2014-06-01

In the 1920s there were still very few fossil human remains to support an evolutionary explanation of human origins. Nonetheless, evolution as an explanatory framework was widely accepted. This led to a search for ancestors in several continents with fierce international competition. With so little fossil evidence available and the idea of a Missing Link as a crucial piece of evidence in human evolution still intact, many actors participated in the scientific race to identify the human ancestor. The curious case of Homo gardarensis serves as an example of how personal ambitions and national pride were deeply interconnected as scientific concerns were sometimes slighted in interwar palaeoanthropology.

In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction and stability and is associated with gigantism.

Science.gov (United States)

Salvatori, Roberto; Radian, Serban; Diekmann, Yoan; Iacovazzo, Donato; David, Alessia; Gabrovska, Plamena; Grassi, Giorgia; Bussell, Anna-Marie; Stals, Karen; Weber, Astrid; Quinton, Richard; Crowne, Elizabeth C; Corazzini, Valentina; Metherell, Lou; Kearney, Tara; Du Plessis, Daniel; Sinha, Ajay Kumar; Baborie, Atik; Lecoq, Anne-Lise; Chanson, Philippe; Ansorge, Olaf; Ellard, Sian; Trainer, Peter J; Balding, David; Thomas, Mark G; Korbonits, Márta

2017-09-01

Mutations in the aryl hydrocarbon receptor-interacting protein ( AIP ) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP -region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to most recent common ancestor (tMRCA) of the derived allele; forward population simulations to estimate current number of allele carriers; proposal of mutation mechanism; protein structure predictions; co-immunoprecipitation and cycloheximide chase experiments. Nine European-origin, unrelated c.805_825dup-positive pedigrees (four familial, five sporadic from the UK, USA and France) included 16 affected (nine gigantism/four acromegaly/two non-functioning pituitary adenoma patients and one prospectively diagnosed acromegaly patient) and nine unaffected carriers. All pedigrees shared a 2.79 Mbp haploblock around AIP with additional haploblocks privately shared between subsets of the pedigrees, indicating the existence of an evolutionarily recent common ancestor, the 'English founder', with an estimated median tMRCA of 47 generations (corresponding to 1175 years) with a confidence interval (9-113 generations, equivalent to 225-2825 years). The mutation occurred in a small tandem repeat region predisposed to slipped strand mispairing. The resulting seven amino-acid duplication disrupts interaction with HSP90 and leads to a marked reduction in protein stability. The c.805_825dup allele, originating from a common ancestor, associates with a severe clinical phenotype and a high frequency of gigantism. The mutation is likely to be the result of slipped strand mispairing and affects protein-protein interactions and AIP protein stability. © 2017 The authors.

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events.

Science.gov (United States)

Urbach, Jonathan M; Ausubel, Frederick M

2017-01-31

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.

The healthy ancestor: embodied inequality and the revitalization of native Hawaiian health

National Research Council Canada - National Science Library

McMullin, Juliet Marie

2010-01-01

"Native Americans, researchers increasingly worry, are disproportionately victims of epidemics and poor health because they "fail" to seek medical care, are "non-compliant" patients, or "lack immunity...

The first suicides: a legacy inherited by parasitic protozoans from prokaryote ancestors.

Science.gov (United States)

Taylor-Brown, Emilie; Hurd, Hilary

2013-04-18

It is more than 25 years since the first report that a protozoan parasite could die by a process resulting in a morphological phenotype akin to apoptosis. Since then these phenotypes have been observed in many unicellular parasites, including trypanosomatids and apicomplexans, and experimental evidence concerning the molecular pathways that are involved is growing. These observations support the view that this form of programmed cell death is an ancient one that predates the evolution of multicellularity. Here we review various hypotheses that attempt to explain the origin of apoptosis, and look for support for these hypotheses amongst the parasitic protists as, with the exception of yeast, most of the work on death mechanisms in unicellular organisms has focussed on them. We examine the role that addiction modules may have played in the original eukaryote cell and the part played by mitochondria in the execution of present day cells, looking for examples from Leishmania spp. Trypanosoma spp. and Plasmodium spp. In addition, the expanding knowledge of proteases, nucleases and other molecules acting in protist execution pathways has enabled comparisons to be made with extant Archaea and bacteria and with biochemical pathways that evolved in metazoans. These comparisons lend support to the original sin hypothesis but also suggest that present-day death pathways may have had multifaceted beginnings.

Evolution of multinucleated Ashbya gossypii hyphae from a budding yeast-like ancestor.

Science.gov (United States)

Schmitz, Hans-Peter; Philippsen, Peter

2011-06-01

In the filamentous ascomycete Ashbya gossypii polarity establishment at sites of germ tube and lateral branch emergence depends on homologues of Saccharomyces cerevisiae factors controlling bud site selection and bud emergence. Maintenance of polar growth involves homologues of well-known polarity factors of budding yeast. To achieve the much higher rates of sustained polar surface expansion of hyphae compared to mainly non-polarly growing yeast buds five important alterations had to evolve. Permanent presence of the polarity machinery at a confined area in the rapidly expanding hyphal tip, increased cytoplasmic space with a much enlarged ER surface for generating secretory vesicles, efficient directed transport of secretory vesicles to and accumulation at the tip, increased capacity of the exocytosis system to process these vesicles, and an efficient endocytosis system for membrane and polarity factor recycling adjacent to the zone of exocytosis. Morphological, cell biological, and molecular aspects of this evolution are discussed based on experiments performed within the past 10 y. Copyright © 2011 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Ancestor Worship in The Logic of Games. How foundational were Aristotle's contributions?

Directory of Open Access Journals (Sweden)

John Woods

2013-12-01

Full Text Available Notwithstanding their technical virtuosity and growing presence in mainstream thinking, game theoretic logics have attracted a sceptical question: "Granted that logic can be done game theoretically, but what would justify the idea that this is the preferred way to do it?'' A recent suggestion is that at least part of the desired support might be found in the Greek dialectical writings. If so, perhaps we could say that those works possess a kind of foundational significance. The relation of being foundational for is interesting in its own right. In this paper, I explore its ancient applicability to relevant, paraconsistent and nonmonotonic logics, before returning to the question of its ancestral tie, or want of one, to the modern logics of games.

The healthy ancestor: embodied inequality and the revitalization of native Hawaiian health

National Research Council Canada - National Science Library

McMullin, Juliet Marie

2010-01-01

..." enjoyed by the "mainstream" population. Challenging this dominant approach to indigenous health, Juliet McMullin shows how it masks more fundamental inequalities that become literally embodied in Native Americans, shifting blame...

The Cult of Ancestors: A Focal Point for Prayers in African Traditional ...

African Journals Online (AJOL)

Religion Dept

The spiritual world of Africa peoples is very densely populated with spiritual beings; ... (2).Who is the focal recipient/addressee in African traditional prayer. ... war or raids, the acceptance of sacrifices and offerings, and ..... weeping, Rachel weeps for her children, she refuses to be .... thought, M. Fortes and G. Dieterlen.

Looking for the most ``primitive'' organism(s) on Earth today: the state of the art

Science.gov (United States)

Forterre, Patrick

1995-02-01

Molecular phylogenetic studies have revealed a tripartite division of the living world into two procaryotic groups, Bacteria and Archaea, and one eucaryotic group, Eucarya. Which group is the most "primitive"? Which groups are sister? The answer to these questions would help to delineate the characters of the last common ancestor to all living beings, as a first step to reconstruct the earliest periods of biological evolution on Earth. The current "Procaryotic dogma" claims that procaryotes are primitive. Since the ancestor of Archaea was most probably a hyperthermophile, and since bacteria too might have originated from hyperthermophiles, the procaryotic dogma has been recently connected to the hot origin of life hypothesis. However, the notion that present-day hyperthermophiles are primitive has been challenged by recent findings, in these unique microorganisms, of very elaborate adaptative devices for life at high temperature. Accordingly, I discuss here alternative hypotheses that challenge the procaryotic dogma, such as the idea of a universal ancestor with molecular features in between those of eucaryotes and procaryotes, or the origin of procaryotes via thermophilic adaptation. Clearly, major evolutionary questions about early cellular evolution on Earth remain to be settled before we can speculate with confidence about which kinds of life might have appeared on other planets.

Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

Directory of Open Access Journals (Sweden)

Jinpeng Wang

2016-10-01

Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

Rosaceous Chamaebatiaria-like foliage from the Paleogene of western North America

Science.gov (United States)

Wolfe, Jack A.; Wehr, Wesley

1988-01-01

Chamaebatiaria and Chamaebatia, two characteristic genera of the Californian floristic province, are traditionally placed in different subfamilies of Rosaceae, Spiraeoideae and Rosoideae, respectively. Analysis of the foliar and reproductive characters of the extant species of these genera indicates that the two genera could be closely related and the assignment of Chamaebatia to Rosoideae invalid. Fossil leaves of lineages of both genera occur in the Paleogene montane floras of the Rocky Mountain region and provide evidence that the two lineages diverged from a common ancestor in the Eocene. The common ancestor probably was adapted to sunny habitats in mesic coniferous forest, and, during the post-Eocene, the two lineages were able to adapt to progressively drier climates. A third extant genus, the east Asian Sorbaria, also appears to be closely related to the California genera and to have been derived from the same common ancestor. New taxa and combinations proposed are: St onebergia columbiana. n. gen. and n. sp.; Salmonensea prefoliolosa (R. W. Br.), n. gen. and n. comb.; Stockeya creedensis (R. W. Br.), n. gen. and n. comb.; Stockeya montana, n. sp.; and Sorbaria wahrhaftigii, n. sp.

Reconstruction of ancestral RNA sequences under multiple structural constraints

Directory of Open Access Journals (Sweden)

Olivier Tremblay-Savard

2016-11-01

Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Ruang Permukiman Tradisional Jawa Berbasis Perlindungan

Directory of Open Access Journals (Sweden)

Endratno Budi Santosa

2016-03-01

Full Text Available Abstract. Traditional Javanese people and society put a lot of philosophy and symbolism in their living practices and daily life. Although in many places this custom is facing great challenges, from historical changes to material developments, there are still people who try to preserve all the traditions inherited from their ancestors. The flexible attitude of the Javanese led to a tradition that emerged as a blend of basic culture and religion (syncretism, which is manifested in a variety of shapes and forms, one of which is the formation of space and the surrounding environment. This paper aims to illustrate as well as compare examples from Javanese spatial culture. There are several basic criteria, including the physical conditions, but the most common is how the spatial organization of a settlement is an attempt or strategy to ask for protection from a higher power, one of which is finding a way to show respect for the ancestors. The study’s findings show that although the macro-concept is usually the same, the material conditions, the history of a settlement’s formation, and local cultural-religious roots led to the specific forms and spatial patterns of specific settlements. Keywords. Traditional settlements, Javanese culture, protection space, ancestor beliefs

Assessment of Flagellate Diversity at Deep-Sea Hydrothermal Vents Using the Combined Approach of Culture-Dependent and Culture-Independent Methods

National Research Council Canada - National Science Library

Atkins, Michael

2000-01-01

.... Molecular and ultrastructural evidence point to one of the isolates. Ancyromonas, as a plausible candidate for the closest relative to the common ancestor of Metazoans, Fungi, and Choanoglagellates...

Reduced swimming performance repeatedly evolves upon loss of migration in landlocked populations of Alewife

Science.gov (United States)

Velotta, Jonathan P.; McCormick, Stephen; Jones, Andrew W.; Schultz, Eric T.

2018-01-01

Whole-organism performance tasks are accomplished by the integration of morphological traits and physiological functions. Understanding how evolutionary change in morphology and physiology influences whole-organism performance will yield insight into the factors that shape its own evolution. We demonstrate that nonmigratory populations of alewife (Alosa pseudoharengus) have evolved reduced swimming performance in parallel, compared with their migratory ancestor. In contrast to theoretically and empirically based predictions, poor swimming among nonmigratory populations is unrelated to the evolution of osmoregulation and occurs despite the fact that nonmigratory alewives have a more fusiform (torpedo-like) body shape than their ancestor. Our results suggest that elimination of long-distance migration from the life cycle has shaped performance more than changes in body shape and physiological regulatory capacity.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers.

Science.gov (United States)

Bloch, Natasha I; Morrow, James M; Chang, Belinda S W; Price, Trevor D

2015-02-01

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors-historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength-sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20 Ma. During this process, the SWS2 gene accumulated six substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Comparison of loline alkaloid gene clusters across fungal endophytes: predicting the co-regulatory sequence motifs and the evolutionary history.

Science.gov (United States)

Kutil, Brandi L; Greenwald, Charles; Liu, Gang; Spiering, Martin J; Schardl, Christopher L; Wilkinson, Heather H

2007-10-01

LOL, a fungal secondary metabolite gene cluster found in Epichloë and Neotyphodium species, is responsible for production of insecticidal loline alkaloids. To analyze the genetic architecture and to predict the evolutionary history of LOL, we compared five clusters from four fungal species (single clusters from Epichloë festucae, Neotyphodium sp. PauTG-1, Neotyphodium coenophialum, and two clusters we previously characterized in Neotyphodium uncinatum). Using PhyloCon to compare putative lol gene promoter regions, we have identified four motifs conserved across the lol genes in all five clusters. Each motif has significant similarity to known fungal transcription factor binding sites in the TRANSFAC database. Conservation of these motifs is further support for the hypothesis that the lol genes are co-regulated. Interestingly, the history of asexual Neotyphodium spp. includes multiple interspecific hybridization events. Comparing clusters from three Neotyphodium species and E. festucae allowed us to determine which Epichloë ancestors are the most likely contributors of LOL in these asexual species. For example, while no present day Epichloë typhina isolates are known to produce lolines, our data support the hypothesis that the E. typhina ancestor(s) of three asexual endophyte species contained a LOL gene cluster. Thus, these data support a model of evolution in which the polymorphism in loline alkaloid production phenotypes among endophyte species is likely due to the loss of the trait over time.

Are palaeoscolecids ancestral ecdysozoans?

Science.gov (United States)

Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

2010-01-01

The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

Nonplantigrade Foot Posture: A Constraint on Dinosaur Body Size.

Directory of Open Access Journals (Sweden)

Tai Kubo

Full Text Available Dinosaurs had functionally digitigrade or sub-unguligrade foot postures. With their immediate ancestors, dinosaurs were the only terrestrial nonplantigrades during the Mesozoic. Extant terrestrial mammals have different optimal body sizes according to their foot posture (plantigrade, digitigrade, and unguligrade, yet the relationship of nonplantigrade foot posture with dinosaur body size has never been investigated, even though the body size of dinosaurs has been studied intensively. According to a large dataset presented in this study, the body sizes of all nonplantigrades (including nonvolant dinosaurs, nonvolant terrestrial birds, extant mammals, and extinct Nearctic mammals are above 500 g, except for macroscelid mammals (i.e., elephant shrew, a few alvarezsauroid dinosaurs, and nondinosaur ornithodirans (i.e., the immediate ancestors of dinosaurs. When nonplantigrade tetrapods evolved from plantigrade ancestors, lineages with nonplantigrade foot posture exhibited a steady increase in body size following Cope's rule. In contrast, contemporaneous plantigrade lineages exhibited no trend in body size evolution and were largely constrained to small body sizes. This evolutionary pattern of body size specific to foot posture occurred repeatedly during both the Mesozoic and the Cenozoic eras. Although disturbed by the end-Cretaceous extinction, species of mid to large body size have predominantly been nonplantigrade animals from the Jurassic until the present; conversely, species with small body size have been exclusively composed of plantigrades in the nonvolant terrestrial tetrapod fauna.

Nonplantigrade Foot Posture: A Constraint on Dinosaur Body Size.

Science.gov (United States)

Kubo, Tai; Kubo, Mugino O

2016-01-01

Dinosaurs had functionally digitigrade or sub-unguligrade foot postures. With their immediate ancestors, dinosaurs were the only terrestrial nonplantigrades during the Mesozoic. Extant terrestrial mammals have different optimal body sizes according to their foot posture (plantigrade, digitigrade, and unguligrade), yet the relationship of nonplantigrade foot posture with dinosaur body size has never been investigated, even though the body size of dinosaurs has been studied intensively. According to a large dataset presented in this study, the body sizes of all nonplantigrades (including nonvolant dinosaurs, nonvolant terrestrial birds, extant mammals, and extinct Nearctic mammals) are above 500 g, except for macroscelid mammals (i.e., elephant shrew), a few alvarezsauroid dinosaurs, and nondinosaur ornithodirans (i.e., the immediate ancestors of dinosaurs). When nonplantigrade tetrapods evolved from plantigrade ancestors, lineages with nonplantigrade foot posture exhibited a steady increase in body size following Cope's rule. In contrast, contemporaneous plantigrade lineages exhibited no trend in body size evolution and were largely constrained to small body sizes. This evolutionary pattern of body size specific to foot posture occurred repeatedly during both the Mesozoic and the Cenozoic eras. Although disturbed by the end-Cretaceous extinction, species of mid to large body size have predominantly been nonplantigrade animals from the Jurassic until the present; conversely, species with small body size have been exclusively composed of plantigrades in the nonvolant terrestrial tetrapod fauna.

Field Screening of Waterlogging Tolerance in Spring Wheat and Spring Barley

Directory of Open Access Journals (Sweden)

Tove Kristina Sundgren

2018-03-01

Full Text Available Improved waterlogging tolerance of wheat and barley varieties may alleviate yield constraints caused by heavy or long-lasting precipitation. The waterlogging tolerance of 181 wheat and 210 barley genotypes was investigated in field trials between 2013 and 2014. A subset of wheat genotypes were selected for yield trials in 2015 and 2016. Our aim was to: (1 characterize the waterlogging tolerance of genotypes with importance for Norwegian wheat and barley breeding, and (2 identify which phenotypic traits that most accurately determine the waterlogging tolerance of wheat in our field trials. Waterlogging tolerance was determined by principal component analysis (PCA where best linear unbiased predictors (BLUPs of the traits chlorosis, relative plant height, heading delay, relative spike number, relative biomass and an overall condition score were used as input variables. Six wheat and five barley genotypes were identified as consistently more tolerant in 2013 and 2014. This included the waterlogging tolerant CIMMYT line CETA/Ae. tauschii (895. Chlorosis and the overall condition score were the traits that best explained the yield response of the genotypes selected for the yield trials. Our results show that early stress symptoms did not necessarily reflect the ability to recover post treatment. Thus, records from full crop cycles appear as fundamental when screening populations with unknown tolerance properties.

What does natural selection lead to?

Indian Academy of Sciences (India)

First page Back Continue Last page Overview Graphics. Changes in the course of time (within the same lineage, ancestors and descendants are seen to belong to different species). Diversity (lineages begin to diverge).

Human genetics: measuring the raw material of evolution.

Science.gov (United States)

Armour, John A L

2009-09-15

By direct sequencing of two Y chromosomes inherited from the same paternal ancestor, a landmark study has derived a good direct estimate for the rate of base substitution mutations on the human Y chromosome.

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

KAUST Repository

Takaku, Yasuharu; Hwang, Jung Shan; Wolf, Alexander; Bö ttger, Angelika; Shimizu, Hiroshi; David, Charles N.; Gojobori, Takashi

2014-01-01

Nerve cells and spontaneous coordinated behavior first appeared near the base of animal evolution in the common ancestor of cnidarians and bilaterians. Experiments on the cnidarian Hydra have demonstrated that nerve cells are essential

Vietnamese Buddhist pagoda in France: “institution-place of memory”. Legitimate power to communicate the memory of exiles

Directory of Open Access Journals (Sweden)

Jérôme GIDOIN

2012-01-01

Full Text Available Vietnamese Buddhism took hold and developed in France partly because it was able to obtain a monopoly on funeral rites and mourning rites. Many exiled families see the interest of this and delegate their ancestor worship to the monks. By combining the spiritual, socio-cultural, eschatological and political domains, and despite whatever generation gaps may exist, the pagoda allows families to reconstruct a social and family ethic in a context of social acculturation. It provides a fitting answer to the question inherent to the migratory context: how to find new symbolic resources outside of Vietnam? And it can thus implement a communication strategy that officialises, in the land of exile, the inextricable link between the pagoda and the assumption of responsibility for the memory of exiled ancestors.

Genealogies in simple models of evolution

International Nuclear Information System (INIS)

Brunet, Éric; Derrida, Bernard

2013-01-01

We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population, in contrast with the linear growth of the neutral case. Moreover for a whole class of models, the statistics of the genealogies are those of the Bolthausen–Sznitman coalescent rather than the Kingman coalescent in the neutral case. For sexual reproduction in the neutral case, the time to reach the first common ancestors for the whole population and the time for all individuals to have all their ancestors in common are also logarithmic in the population size, as predicted by Chang in 1999. We discuss how these times are modified by introducing selection in a simple way. (paper)

The ancestral selection graph under strong directional selection.

Science.gov (United States)

Pokalyuk, Cornelia; Pfaffelhuber, Peter

2013-08-01

The ancestral selection graph (ASG) was introduced by  Neuhauser and Krone (1997) in order to study populations of constant size which evolve under selection. Coalescence events, which occur at rate 1 for every pair of lines, lead to joint ancestry. In addition, splitting events in the ASG at rate α, the scaled selection coefficient, produce possible ancestors, such that the real ancestor depends on the ancestral alleles. Here, we use the ASG in the case without mutation in order to study fixation of a beneficial mutant. Using our main tool, a reversibility property of the ASG, we provide a new proof of the fact that a beneficial allele fixes roughly in time (2logα)/α if α is large. Copyright © 2012 Elsevier Inc. All rights reserved.

On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype.

Science.gov (United States)

Dey, Gautam; Thattai, Mukund; Baum, Buzz

2016-07-01

If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although 'Loki' cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Journeys of our ancestors: Conservation science approaches to the analysis of cultural material

Science.gov (United States)

O'Grady, Caitlin Rose

The application and use of non-destructive portable x-ray fluorescence (XRF) analysis is a critical tool in the preservation and interpretation of cultural material. Portable XRF instrumentation produce elemental compositional data that is used to reconstruct current artifact composition, which can be related to materials and methods of manufacture, technological practice, as well as object condition and presence of corrosion surfaces. Portable XRF analysis is used to assess a variety of material classes utilized in artifact manufacture. The dissertation research is based on a series of three case studies that represent typical groups of material culture commonly encountered in conservation and conservation science research. Conservators and conservation scientists frequently undertake analysis and interpretation of disparate groups of materials. Often, these objects are tied together by research questions or themes directed by outside influences including preservation issues requiring action; curatorial research interests; museum exhibition programs; as well as many other cultural heritage stakeholders. To this end, both non-destructive and destructive tools that provide measurements of interest play critical roles in analysis. The case studies have been designed to answer common compositional questions relating to (a) bulk analysis of Chinese coins, (b) characterization of Southwestern ceramic colorants, and, (c) chemical examination of post-depositional manganese dioxide accretions occurring on archaeological ceramic materials. They evaluate the value of data produced using effectiveness of non-destructive portable XRF analysis for the interpretation of archaeological materials. The case studies provide a template for the development of conservation science research, predicated on object preservation, which produce meaningful data for the interpretation and conservation of the analyzed archaeological artifacts. Portable XRF provides useful data that is used to successfully interpret archaeological materials through (a) classification of metal alloys that can be related to published coin data, (b) identification of ceramic colorants and production technologies, and, (c) characterization of post-depositional product composition when used with established visual typologies.

The Poetics of the Ancestor Songs of the Tz’utujil Maya of Guatemala

Directory of Open Access Journals (Sweden)

Linda O’Brien-Rothe

2010-04-01

Full Text Available This essay attempts to define the relationship between a song tradition that survives in the Mayan highlands of Guatemala, and 16th century poetic Mayan literature. This song tradition of Santiago Atitlán, Guatemala is slowly disappearing as the socio-cultural context in which it flourished changes. By comparing the poetics of the song texts (including their rhythmic structure, versification, and use of poetic devices such as assonance, alliteration and onomatopoeia to the poetics of the Popol Vuh, a K’iché Maya text probably copied from a manuscript that predates the Spanish invasion, a continuity is discovered that places the song texts squarely within the tradition of Mayan literature and suggests common origins.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

Science.gov (United States)

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-07-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

How We Got Here: Evolutionary Changes in Skull Shape in Humans & Their Ancestors

Science.gov (United States)

Price, Rebecca M.

2012-01-01

This activity uses inquiry to investigate how large changes in shape can evolve from small changes in the timing of development. Students measure skull shape in fetal, infant, juvenile, and adult chimpanzees and compare them to adult skulls of "Homo sapiens," "Homo erectus," and "Australopithecus afarensis." They conclude by re-interpreting their…

Evidence for a single loss of mineralized teeth in the common avian ancestor

DEFF Research Database (Denmark)

Meredith, Robert W.; Zhang, Guojie; Gilbert, M. Thomas P.

2014-01-01

Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and process food.We performed comparative genomic ...

Use of indigenous knowledge and traditional practices in fisheries ...

African Journals Online (AJOL)

MESP

changes in social structures, immigration and advent of new religions, adoption of new resource ... reflect social organisation and power structure. ..... reported that traditional leaders over two ... sacrifices to their ancestors when fish was scarce ...

Using maps in genealogy

Science.gov (United States)

,

2002-01-01

In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

Editorial

African Journals Online (AJOL)

denise

In a recent article in American Psychologist, Howard. Kendler .... present analyses of ancestor dreams within the context of .... an end to. This existential dilemma of meaningless ... Levinas thematizes in his own analysis of the ethical relation.

REARRANGEMENT IN THE B-GENOME FROM DIPLOID PROGENITOR TO WHEAT ALLOPOLYPOLID

Directory of Open Access Journals (Sweden)

Salina E.A.

2012-08-01

Full Text Available Three key periods that were accompanied by considerable rearrangements in the B genome of wheat and its progenitor can be considered. The first period covers the period from the divergence of diploid Triticum and Aegilops species from their common progenitor (2.5–6 million years ago to formation of the tetraploid T. diccocoides (about 500 thousand years ago. Significant genomic rearrangements in the diploid progenitor of the B genome, Ae. speltoides (SS genome, involved a considerable amplification of repeated DNA sequences, which led to an increase in the number of heterochromatin blocks on chromosomes relative to other diploid Aegilops and Triticum species. Our analysis has demonstrated that during this period the Spelt1 repeats intensively amplified as well as several mobile elements proliferated, in particular, the genome-specific gypsy LTR-retrotransposon Fatima and CACTA DNA-transposon Caspar. The second period in the B-genome evolution was associated with the emergence of tetraploid (BBAA genome and its subsequent evolution. The third most important event leading to the next rearrangement of the B genome took place relatively recently, 7000–9500 years ago, being associated with the emergence of hexaploid wheat with the genomic formula BBAADD. The evolution of the B/S genome involved intergenomic and intragenomic translocations and chromosome inversions. So far, five rearrangements in the B-genome chromosomes of polyploid wheats has been observed and described; the majority of them took place during the formation and evolution of tetraploid species. The mapping of the S-genome chromosomes and comparison with the B-genome chromosome maps have demonstrated that individual rearrangements pre-existed in Ae. speltoides; moreover, Ae. speltoides is polymorphic for these rearrangements.Chromosome 5B is nearly 870 Mbp (5BL = 580 Mbp and 5BS = 290 Mbp and is known to carry important genes controlling the key aspects of wheat biology, in

Know Your Personal Computer

Indian Academy of Sciences (India)

computer with IBM PC .... read by a human and not translated by a compiler are called .... by different stages of education becomes a computer scientist. ... ancestors knew and carried out the semantic actions without question or comment.

Internal and ancestral controls of cell-generation times

Science.gov (United States)

Kubitschek, H. E.

1969-01-01

Lateral and longitudinal correlations between related cells reveal associations between the generation times of cells for an intermediate period /three generations in bacteral cultures/. Generation times of progeny are influenced by nongenetic factors transmitted from their ancestors.

How the mitochondrion was shaped by radical differences in substrates: what carnitine shuttles and uncoupling tell us about mitochondrial evolution in response to ROS

NARCIS (Netherlands)

Speijer, Dave

2014-01-01

As free-living organisms, alpha-proteobacteria produce reactive oxygen species (ROS) that diffuse into the surroundings; once constrained inside the archaeal ancestor of eukaryotes, however, ROS production presented evolutionary pressures - especially because the alpha-proteobacterial symbiont made

From Neurons to Night of the Living Dead

DEFF Research Database (Denmark)

Clasen, Mathias

2012-01-01

Life in prehistoric times was dangerous. Our evolutionary ancestors faced a range of potentially threatening organisms: carnivorous predators, venomous animals, invisible pathogens, and hostile conspecifics. Thus, natural selection has produced a species-typical cognitive architecture for danger-...

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

KAUST Repository

Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaë l; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T.

2018-01-01

and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication.

Science.gov (United States)

Wang, Ming-Shan; Zhang, Rong-Wei; Su, Ling-Yan; Li, Yan; Peng, Min-Sheng; Liu, He-Qun; Zeng, Lin; Irwin, David M; Du, Jiu-Lin; Yao, Yong-Gang; Wu, Dong-Dong; Zhang, Ya-Ping

2016-05-01

As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.

diagnosis and treatment of heart failure in the community

African Journals Online (AJOL)

Enrique

gestion/fluid overload) and institution of basic, standard treatment where appro- priate. .... measures. These include: ..... According to a study of our ancestors' teeth, we evolved into meat-eaters around 2.5 million years ago. Analysis by an ...

The organellar genome and metabolic potential of the hydrogen- producing mitochondrion of Nyctotherus ovalis

NARCIS (Netherlands)

J.H.P. Hackstein (Johannes); C. Burgtorf; B.E. Dutilh (Bas); I. Duarte (Isabel); G.W.M. van der Staay (Georg); R.M. de Graaf (Rob); J.W.P. Kuiper (Jan); M. Huynen (Martijn); T.A. van Alen (Theo); G. Ricard (Guenola); A.G.M. Tielens (Aloysius)

2011-01-01

textabstractAbstract It is generally accepted that hydrogenosomes (hydrogen-producing organelles) evolved from a mitochondrial ancestor. However, until recently, only indirect evidence for this hypothesis was available. Here, we present the almost complete genome of the hydrogen-producing

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy

KAUST Repository

Reid, Adam James; Vermont, Sarah J.; Cotton, James A.; Harris, David; Hill-Cawthorne, Grant A.; Kö nen-Waisman, Stephanie; Latham, Sophia M.; Mourier, Tobias; Norton, Rebecca; Quail, Michael A.; Sanders, Mandy; Shanmugam, Dhanasekaran; Sohal, Amandeep; Wasmuth, James D.; Brunk, Brian; Grigg, Michael E.; Howard, Jonathan C.; Parkinson, John; Roos, David S.; Trees, Alexander J.; Berriman, Matthew; Pain, Arnab; Wastling, Jonathan M.

2012-01-01

and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion

Body composition in Pan paniscus compared with Homo sapiens has implications for changes during human evolution.

Science.gov (United States)

Zihlman, Adrienne L; Bolter, Debra R

2015-06-16

The human body has been shaped by natural selection during the past 4-5 million years. Fossils preserve bones and teeth but lack muscle, skin, fat, and organs. To understand the evolution of the human form, information about both soft and hard tissues of our ancestors is needed. Our closest living relatives of the genus Pan provide the best comparative model to those ancestors. Here, we present data on the body composition of 13 bonobos (Pan paniscus) measured during anatomical dissections and compare the data with Homo sapiens. These comparative data suggest that both females and males (i) increased body fat, (ii) decreased relative muscle mass, (iii) redistributed muscle mass to lower limbs, and (iv) decreased relative mass of skin during human evolution. Comparison of soft tissues between Pan and Homo provides new insights into the function and evolution of body composition.

A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites

Directory of Open Access Journals (Sweden)

Yne de Vries

2012-01-01

Full Text Available Fanconi anemia (FA is a recessive DNA instability disorder associated with developmental abnormalities, bone marrow failure, and a predisposition to cancer. Based on their sensitivity to DNA cross-linking agents, FA cells have been assigned to 15 complementation groups, and the associated genes have been identified. Founder mutations have been found in different FA genes in several populations. The majority of Dutch FA patients belongs to complementation group FA-C. Here, we report 15 patients of Dutch ancestry and a large Canadian Manitoba Mennonite kindred carrying the FANCC c.67delG mutation. Genealogical investigation into the ancestors of the Dutch patients shows that these ancestors lived in four distinct areas in The Netherlands. We also show that the Dutch and Manitoba Mennonite FANCC c.67delG patients share the same haplotype surrounding this mutation, indicating a common founder.

[Familial occurrence of diprosopus in German Holstein calves].

Science.gov (United States)

Schulze, Ursula; Kuiper, Heidi; Doeleke, Renate; Ulrich, Reiner; Gerdwilker, Axel; Distl, Ottmar

2006-01-01

Diprosopus was diagnosed in six German Holstein calves born on different dairy farms. The degree of facial duplication varied from a partial doubling of the nostrils and upper jaw to complete duplication of the face with formation of two mouths, four eyes and four ears. Further calves descending from the same parents or dams and calves from the same farms were not affected. A joint pedigree was ascertained for the calves with diprosopus. Furthermore, a previously reported case of diprosopus could be traced back to the same ancestors of this pedigree. Consequently, we detected the first time a familial accumulation of diprosopus. Since the ancestors showed no signs of diprosopus and the frequency of diprosopus in German Holsteins is presumably low, an oligogenic inheritance is likely. Recessive genes or a combination of recessive and dominant genes may cause this anomaly.

A phylogenetic view of the Out of Asia/Eurasia and Out of Africa hypotheses in the light of recent molecular and palaeontological finds.

Science.gov (United States)

Árnason, Úlfur

2017-09-05

The substantiality of the Out of Africa hypothesis was addressed in the light of recent genomic analysis of extant humans (Homo sapiens sapiens, Hss) and progress in Neanderthal palaeontology. The examination lent no support to the commonly assumed Out of Africa scenario but favoured instead a Eurasian divergence between Neanderthals and Hss (the Askur/Embla hypothesis) and an Out of Asia/Eurasia hypothesis according to which all other parts of the world were colonized by Hss migrations from Asia. The examination suggested furthermore that the ancestors of extant KhoeSan and Mbuti composed the first Hss dispersal(s) into Africa and that the ancestors of Yoruba made up a later wave into the same continent. The conclusions constitute a change in paradigm for the study of human evolution. Copyright © 2017. Published by Elsevier B.V.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

Science.gov (United States)

Onimaru, Koh; Kuraku, Shigehiro

2018-03-16

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as 'chronological reconstruction of ohnolog functions (CHROF)'. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

Evolution of dinosaur epidermal structures.

Science.gov (United States)

Barrett, Paul M; Evans, David C; Campione, Nicolás E

2015-06-01

Spectacularly preserved non-avian dinosaurs with integumentary filaments/feathers have revolutionized dinosaur studies and fostered the suggestion that the dinosaur common ancestor possessed complex integumentary structures homologous to feathers. This hypothesis has major implications for interpreting dinosaur biology, but has not been tested rigorously. Using a comprehensive database of dinosaur skin traces, we apply maximum-likelihood methods to reconstruct the phylogenetic distribution of epidermal structures and interpret their evolutionary history. Most of these analyses find no compelling evidence for the appearance of protofeathers in the dinosaur common ancestor and scales are usually recovered as the plesiomorphic state, but results are sensitive to the outgroup condition in pterosaurs. Rare occurrences of ornithischian filamentous integument might represent independent acquisitions of novel epidermal structures that are not homologous with theropod feathers. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The challenge that Confucian filial piety poses for Korean churches

African Journals Online (AJOL)

2014-04-30

Apr 30, 2014 ... Thus, Korean Confucians and non-Christians have criticised. Christianity as a .... The piel form is primarily a declarative meaning of 'honour or .... Confucian ancestor worship is not just the memory of the dead father and ...

The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis.

Science.gov (United States)

Wang, Dan; Zhao, Jieyu; Bai, Yan; Ao, You; Guo, Changhong

2017-08-10

Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS-3C and CS-3C3C, 48.68% and 48.65%, respectively) were significantly increased when compared to common wheat CS (41.31%) and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted-repeat transposable elements), LTR-retrotransposon WIS-1p and retrotransposon Gypsy , respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis

Directory of Open Access Journals (Sweden)

Dan Wang

2017-08-01

Full Text Available Gametocidal (Gc chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS–3C and CS–3C3C, 48.68% and 48.65%, respectively were significantly increased when compared to common wheat CS (41.31% and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted–repeat transposable elements, LTR-retrotransposon WIS-1p and retrotransposon Gypsy, respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

Carbohydrate self-recognition mediates marine sponge cellular adhesion

NARCIS (Netherlands)

Vliegenthart, J.F.G.; Haseley, S.R.; Vermeer, H.J.; Kamerling, J.P.

2001-01-01

Sponges (Porifera), the simplest and earliest multicellular organisms, are thought to have evolved from their unicellular ancestors about 1 billion years ago by developing cell-recognition and adhesion mechanisms to discriminate against 'non-self.' Consequently, they are used as models for

multilingualism and the ethnic identity of the ette people

African Journals Online (AJOL)

chy

Bilingualism/multilingualism will be discussed in section four; while section ... In the past, our ancestors moved from one place to the other in search of ... The concept of ethnicity, however, encompasses a lot of meaning so that its definition is.

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

Science.gov (United States)

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted…

Indilinga: African Journal of Indigenous Knowledge Systems - Vol 8 ...

African Journals Online (AJOL)

The Role Of The Ancestors In Healing · EMAIL FULL TEXT EMAIL FULL TEXT DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. S Edwards, N Makunga, J Thwala, B Mbele. http://dx.doi.org/10.4314/indilinga.v8i1.48234 ...

Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

DEFF Research Database (Denmark)

Kutty, Sujatha Narayanan; Pont, Adrian C.; Meier, Rudolf

2014-01-01

split within this family. The ancestral larval feeding habit is reconstructed to be saprophagy with more specialised coprophagous saprophagy, phytophagy, and carnivory evolving multiple times from saprophagous ancestors. The origins of carnivory in larvae are significantly correlated with a reduction...

A genomic history of Aboriginal Australia

DEFF Research Database (Denmark)

Malaspinas, Anna-Sapfo; Westaway, Michael C.; Muller, Craig

2016-01-01

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors...

124 The Relevance of Ali (Earth Deity): Ritual Forms And Processes ...

African Journals Online (AJOL)

Tracie1

remained a rhythm of significance in man's response to the sacred and his experience within the .... prototypes the repetition of the action of divine beings or mythical ancestors,” a .... changing and moving concerns of life. For the African, the ...

The ethnification of electoral conflicts in Kenya: Options for positive ...

African Journals Online (AJOL)

these leaders turned elections into structures for rewarding loyalists and punishing ... 'transition election', realised the democratic intentions of regime change and assured the .... In addition, Non-Governmental Organisations (NGOs) in Kenya .... ceremonies involve making sacrifices to the ancestors aimed at protecting.

The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria

Directory of Open Access Journals (Sweden)

Raoult Didier

2011-10-01

Full Text Available Abstract Background Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. We used the mitochondria of four distinct organisms, Reclinomonas americana, Homo sapiens, Saccharomyces cerevisiae and multichromosome Pediculus humanus, and attempted to identify the origin of each mitochondrial gene. Results Our results suggest that the origin of mitochondrial genes is not limited to the Rickettsiales and that the creation of these genes did not occur in a single event, but through multiple successive events. Some of these events are very old and were followed by events that are more recent and occurred through the addition of elements originating from current species. The points in time that the elements were added and the parental species of each gene in the mitochondrial genome are different to the individual species. These data constitute strong evidence that mitochondria do not have a single common ancestor but likely have numerous ancestors, including proto-Rickettsiales, proto-Rhizobiales and proto-Alphaproteobacteria, as well as current alphaproteobacterial species. The analysis of the multichromosome P. humanus mitochondrion supports this mechanism. Conclusions The most plausible scenario of the origin of the mitochondrion is that ancestors of Rickettsiales and Rhizobiales merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the Rickettsiales and Rhizobiales cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for

Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation

Directory of Open Access Journals (Sweden)

Guorong Zhang

2018-04-01

Full Text Available Wheat streak mosaic virus (WSMV causes streak mosaic disease in wheat (Triticum aestivum L. and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of

Comparative genetic mapping reveals synteny and collinearity between the American cranberry and diploid blueberry genomes

Science.gov (United States)

Cranberry (section Oxcycoccus) and blueberry (section Cyanococcus), are closely related and recently domesticated fruit crops in the genus Vaccinium (family Ericaceae). Both the Oxycoccus and Cyanococcus sections are presumed to have an American origin and likely evolved from a common ancestor; howe...

Compiler generation based on grammar inheritance

NARCIS (Netherlands)

Aksit, Mehmet; Mostert, Rene; Haverkort, Boudewijn R.H.M.

1990-01-01

The concept of grammar inheritance is introduced. Grammar inheritance is a structural organization of grammar rules by which a grammar inherits rules from ancestor grammars or may have its own rules inherited by descendant grammars. Grammar inheritance supports reusability and extensibility of

The Neolithic Revolution from a price-theoretic perspective

DEFF Research Database (Denmark)

Ricardo Andrés Guzmán, Jacob Weisdorf; Weisdorf, Jacob Louis

2011-01-01

The adoption of agriculture during the Neolithic period triggered the first demographic explosion in history. When fertility returned to its original level, agriculturalists were more numerous, more poorly nourished, and worked longer hours than their hunter–gatherer ancestors. We develop a dynamic...

Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity

NARCIS (Netherlands)

N. Nagle (Nano); M. van Oven (Mannis); S. Wilcox (Stephen); S. Van Holst Pellekaan (Sheila); C. Tyler-Smith (Chris); Y. Xue (Yali); K. Ballantyne (Kaye); L. Wilcox (Leah); L. Papac (Luka); K. Cooke (Karen); R.A.H. van Oorschot (Roland ); P. McAllister (Peter); L. Williams (Lesley); M.H. Kayser (Manfred); R.J. Mitchell (R. John)

2017-01-01

textabstractAboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ∼55 thousand years ago. Genetic studies, though limited, have demonstrated

Oral Tradition as the Literary Skeleton of African Novels: A Study of ...

African Journals Online (AJOL)

s way of life, often expressed in what they do (social functions and roles); what they think (their philosophy of life about birth, death, God, heaven, hell, health, ancestors, wealth, poverty etc) and what they have (the material aspects of culture ...

LUCA, or just a conserved Archaeon?: Comments on Xue et al. (2003)

Czech Academy of Sciences Publication Activity Database

Čejchan, Petr

2004-01-01

Roč. 333, Supplement (2004), s. 47-50 ISSN 0378-1119 R&D Projects: GA ČR(CZ) GA205/03/1124 Keywords : Last universal common ancestor * universal tree * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.705, year: 2004

A thermodynamical measure of cooperativity: application to hemoglobin

International Nuclear Information System (INIS)

Jacchieri, S.G.; Ferreira, R.C.

1984-01-01

A comparative analysis of the heat requirements for dioxygen exchange is made for hemoglobin and myoglobin, the latter taken as the prototype of the vertebrate hemoglobin's ancestor. it is shown that cooperativity manifests itself also in terms of energy utilization. (Author) [pt

The Function and Evolution of the Halloween Genes; the Pathway to the Arthropod Molting Hormone. In Ecdysone, Structures and Functions

DEFF Research Database (Denmark)

Gilbert, Lawrence; Rewitz, Kim

2009-01-01

, Coleoptera, Hymenoptera and other Diptera allowed the development of a phylogenetic scheme for this gene family and suggests that the Halloween genes and vertebrate steroidogenic P450s originated from common ancestors that were perhaps destined for steroidogenesis, and arose before the deuterostome...

Linking spatial processes to life-history evolution of insect parasitoids

NARCIS (Netherlands)

Hoffmeister, T.S.; Roitberg, B.D.; Vet, L.E.M.

2005-01-01

Understanding the evolutionary transition from solitary to group living in animals is a profound challenge to evolutionary ecologists. A special case is found in insect parasitoids, where a tolerant gregarious larval lifestyle evolved from an intolerant solitary ancestor. The conditions for this

THE AMINO-ACID-SEQUENCE OF IGUANA (IGUANA-IGUANA) PANCREATIC RIBONUCLEASE

NARCIS (Netherlands)

ZHAO, W; BEINTEMA, JJ; HOFSTEENGE, J

1994-01-01

The pyrimidine-specific ribonuclease superfamily constitutes a group of homologous proteins so far found only in higher vertebrates. Four separate families are found in mammals, which have resulted from gene duplications in mammalian ancestors. To learn more about the evolutionary history of this

The Neolithic Revolution from a Price-Theoretic Perspective

DEFF Research Database (Denmark)

Guzmán, Ricardo Andrés; Weisdorf, Jacob Louis

The adoption of agriculture during the Neolithic period triggered the first demographic explosion in history. When fertility returned to its original level, agriculturalists were more numerous, more poorly nourished, and worked longer hours than their hunter-gatherer ancestors. We develop a dynam...

The emerging functions of histone demethylases

DEFF Research Database (Denmark)

Agger, Karl; Christensen, Jesper; Cloos, Paul Ac

2008-01-01

characteristic features evolve from the same ancestor, despite identical genomic material. The characterization of several enzymes catalyzing histone lysine methylation have supported this concept by showing the requirement of these enzymes for normal development and their involvement in diseases such as cancer...

Sickle Cell Research: Yesterday, Today, and Tomorrow | NIH MedlinePlus the Magazine

Science.gov (United States)

... whose families come from, or have ancestors from, sub-Saharan Africa, South or Central America (especially Panama), Caribbean islands, Mediterranean countries (such as Turkey, Greece, and Italy), India, and Saudi Arabia. Ask Your Health Professional If you, your child, or another loved ...

R-ES-ONANCE--IOc-tO-ber-19-9-7

Indian Academy of Sciences (India)

A clone refers to a population of cells or organisms which were derived asexually from a single ancestor. ... Hence, the nuclei from early embryos seemed to ... have come from a stem cell, which had ... It remains to be seen if a human adult.

Evolutionary heritage influences amazon tree ecology

NARCIS (Netherlands)

Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of

Unseen and unsung heroes: The microbes

Digital Repository Service at National Institute of Oceanography (India)

Raghukumar, S.

Fungi are larger microorganisms and their bodies are mostly filamentous, the filaments being called hyphae. It is now believed that fungi evolved from an ancestor that was also common to animals. The width of the fungal hyphae is just about 3 to 5...

Origin of clothing lice indicates early clothing use by anatomically modern humans in Africa.

Science.gov (United States)

Toups, Melissa A; Kitchen, Andrew; Light, Jessica E; Reed, David L

2011-01-01

Clothing use is an important modern behavior that contributed to the successful expansion of humans into higher latitudes and cold climates. Previous research suggests that clothing use originated anywhere between 40,000 and 3 Ma, though there is little direct archaeological, fossil, or genetic evidence to support more specific estimates. Since clothing lice evolved from head louse ancestors once humans adopted clothing, dating the emergence of clothing lice may provide more specific estimates of the origin of clothing use. Here, we use a Bayesian coalescent modeling approach to estimate that clothing lice diverged from head louse ancestors at least by 83,000 and possibly as early as 170,000 years ago. Our analysis suggests that the use of clothing likely originated with anatomically modern humans in Africa and reinforces a broad trend of modern human developments in Africa during the Middle to Late Pleistocene.

Niche construction drives social dependence in hermit crabs.

Science.gov (United States)

Laidre, Mark E

2012-10-23

Organisms can receive not only a genetic inheritance from their ancestors but also an ecological inheritance, involving modifications their ancestors made to the environment through niche construction. Ecological inheritances may persist as a legacy, potentially generating selection pressures that favor sociality. Yet, most proposed cases of sociality being impacted by an ecological inheritance come from organisms that live among close kin and were highly social before their niche construction began. Here, I show that in terrestrial hermit crabs (Coenobita compressus)--organisms that do not live with kin and reside alone, each in its own shell--niche-construction drives social dependence, such that individuals can only survive in remodeled shells handed down from conspecifics. These results suggest that niche construction can be an important initiator of evolutionary pressures to socialize, even among unrelated and otherwise asocial organisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

La ordenación del territorio en la Prehistoria: El caso de la Aldea ceremonial de Orongo en Isla de Pascua.

Directory of Open Access Journals (Sweden)

María Eugenia Pallarés Torres

2009-09-01

Rapanui culture was characterized by a strong relationship with the ancestors and the origins, favoring the presence of the ancestors and the cosmic relations, with the sea and the sky means that connect with life and the future. The territory was the scene where ideas and concepts were introduced, which materialized through buildings, taking environmental variables, promoted a respectful way of living and inspired by the environment and faithful to the beliefs. In all interventions, there is a duality in remaining private and intentions of the whole community, with a model that divided between clans entire surface of the island, maintaining a communication network through private domains, connecting all population with important and unique areas, both from the perspective ceremonial, as the fund-raising. The settlement pattern is carried out throughout the territory, adapting to the topography, including ceremonial area, housing, culture and storage.

Expression, purification and crystallization of the ancestral androgen receptor-DHT complex.

Science.gov (United States)

Colucci, Jennifer K; Ortlund, Eric A

2013-09-01

Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

Energy Technology Data Exchange (ETDEWEB)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.; Overall, Christopher C.; Lee, Joon-Yong; Zucker, Jeremy D.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

2017-03-02

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats.

Science.gov (United States)

Thiagavel, Jeneni; Cechetto, Clément; Santana, Sharlene E; Jakobsen, Lasse; Warrant, Eric J; Ratcliffe, John M

2018-01-08

Substantial evidence now supports the hypothesis that the common ancestor of bats was nocturnal and capable of both powered flight and laryngeal echolocation. This scenario entails a parallel sensory and biomechanical transition from a nonvolant, vision-reliant mammal to one capable of sonar and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation. Further, we find that among extant predatory bats (all of which use laryngeal echolocation), those with putatively less sophisticated biosonar have relatively larger eyes than do more sophisticated echolocators. We contend that signs of ancient trade-offs between vision and echolocation persist today, and that non-echolocating, phytophagous pteropodid bats may retain some of the necessary foundations for biosonar.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Science.gov (United States)

Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

2013-01-01

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

Coevolution of aah: A dps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

Directory of Open Access Journals (Sweden)

Liyan Ping

2012-01-01

Full Text Available A protein named AAH was isolated from the bacterium Microbacterium arborescens SE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of the aah gene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny of dps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. The aah gene had evolved new function but still retained the typical dodecameric structure.

On Earth, there would be a number of fundamental kinds of primary cells - cellular domains - greater than or equal to four.

Science.gov (United States)

Di Giulio, Massimo

2018-04-14

In the studies regarding the deep nodes of the tree of life, there is an assumption that might be false. Usually, it is assumed that these nodes - that is to say, those for example regarding the ancestors of bacteria and archaea - are believed to be completely evolved cells and not protocells. In other words, in these studies, it is rarely stressed that, on the contrary, these nodes might correspond to evolutionary stages of premature cells, namely, progenotes. This observation has extremely relevant consequences. Indeed, if the nodes, for example, of the ancestors of bacteria and archaea would correspond to progenotic evolutionary stages, then this should imply that the number of fundamental kinds of primary cells (cellular domains), present on Earth, would be at least four and not two or three as it is currently believed. As a matter of fact, if these two nodes would correspond to two progenotes then, evidently, the fully evolved cells (genotes) - to which we should refer to be able to establish how many fundamental kinds of primary cells are present on Earth - would characterize less deep nodes of these two. Thus, since there is a strong evidence that the ancestors of archaea and bacteria have been of progenotes, these reasonings would assume a particular importance. For instance, it is maintained that one of these fundamental primary cells might be represented by the typical cell of superphylum of the DPANN. In other words, the DPANN superphylum might be a so far non-recognized cellular domain of life. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Genealogical Look at Shared Ancestry on the X Chromosome.

Science.gov (United States)

Buffalo, Vince; Mount, Stephen M; Coop, Graham

2016-09-01

Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism data sets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We hope to learn additional information about recent ancestry through shared IBD segments on the X chromosome, but currently lack the theoretical framework to use this information fully. Here, we fill this gap by developing probability distributions for the number and length of X chromosome segments shared IBD between an individual and an ancestor k generations back, as well as between half- and full-cousin relationships. Due to the inheritance pattern of the X and the fact that X homologous recombination occurs only in females (outside of the pseudoautosomal regions), the number of females along a genealogical lineage is a key quantity for understanding the number and length of the IBD segments shared among relatives. When inferring relationships among individuals, the number of female ancestors along a genealogical lineage will often be unknown. Therefore, our IBD segment length and number distributions marginalize over this unknown number of recombinational meioses through a distribution of recombinational meioses we derive. By using Bayes' theorem to invert these distributions, we can estimate the number of female ancestors between two relatives, giving us details about the genealogical relations between individuals not possible with autosomal data alone. Copyright © 2016 by the Genetics Society of America.

Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene: Implications for crop plant evolution and areas of origin

Science.gov (United States)

Sanjur, Oris I.; Piperno, Dolores R.; Andres, Thomas C.; Wessel-Beaver, Linda

2002-01-01

We have investigated the phylogenetic relationships among six wild and six domesticated taxa of Cucurbita using as a marker an intron region from the mitochondrial nad1 gene. Our study represents one of the first successful uses of a mtDNA gene in resolving inter- and intraspecific taxonomic relationships in Angiosperms and yields several important insights into the origins of domesticated Cucurbita. First, our data suggest at least six independent domestication events from distinct wild ancestors. Second, Cucurbita argyrosperma likely was domesticated from a wild Mexican gourd, Cucurbita sororia, probably in the same region of southwest Mexico that gave rise to maize. Third, the wild ancestor of Cucurbita moschata is still unknown, but mtDNA data combined with other sources of information suggest that it will probably be found in lowland northern South America. Fourth, Cucurbita andreana is supported as the wild progenitor of Cucurbita maxima, but humid lowland regions of Bolivia in addition to warmer temperate zones in South America from where C. andreana was originally described should possibly be considered as an area of origin for C. maxima. Fifth, our data support other molecular results that indicate two separate domestications in the Cucurbita pepo complex. The potential zone of domestication for one of the domesticated subspecies, C. pepo subsp. ovifera, includes eastern North America and should be extended to northeastern Mexico. The wild ancestor of the other domesticated subspecies, C. pepo subsp. pepo, is undiscovered but is closely related to C. pepo subsp. fraterna and possibly will be found in southern Mexico. PMID:11782554

Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene: Implications for crop plant evolution and areas of origin.

Science.gov (United States)

Sanjur, Oris I; Piperno, Dolores R; Andres, Thomas C; Wessel-Beaver, Linda

2002-01-08

We have investigated the phylogenetic relationships among six wild and six domesticated taxa of Cucurbita using as a marker an intron region from the mitochondrial nad1 gene. Our study represents one of the first successful uses of a mtDNA gene in resolving inter- and intraspecific taxonomic relationships in Angiosperms and yields several important insights into the origins of domesticated Cucurbita. First, our data suggest at least six independent domestication events from distinct wild ancestors. Second, Cucurbita argyrosperma likely was domesticated from a wild Mexican gourd, Cucurbita sororia, probably in the same region of southwest Mexico that gave rise to maize. Third, the wild ancestor of Cucurbita moschata is still unknown, but mtDNA data combined with other sources of information suggest that it will probably be found in lowland northern South America. Fourth, Cucurbita andreana is supported as the wild progenitor of Cucurbita maxima, but humid lowland regions of Bolivia in addition to warmer temperate zones in South America from where C. andreana was originally described should possibly be considered as an area of origin for C. maxima. Fifth, our data support other molecular results that indicate two separate domestications in the Cucurbita pepo complex. The potential zone of domestication for one of the domesticated subspecies, C. pepo subsp. ovifera, includes eastern North America and should be extended to northeastern Mexico. The wild ancestor of the other domesticated subspecies, C. pepo subsp. pepo, is undiscovered but is closely related to C. pepo subsp. fraterna and possibly will be found in southern Mexico.

Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

Science.gov (United States)

Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

2009-10-01

We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa.

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

Science.gov (United States)

Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

2016-10-06

Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

Evidence of ancient genome reduction in red algae (Rhodophyta).

Science.gov (United States)

Qiu, Huan; Price, Dana C; Yang, Eun Chan; Yoon, Hwan Su; Bhattacharya, Debashish

2015-08-01

Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle. © 2015 Phycological Society of America.

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land.

Science.gov (United States)

Emiliani, Giovanni; Fondi, Marco; Fani, Renato; Gribaldo, Simonetta

2009-02-16

The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified. We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments. Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.

The Amborella vacuolar processing enzyme family

Directory of Open Access Journals (Sweden)

Valérie ePoncet

2015-08-01

Full Text Available Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs. In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type of seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013. In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella’s genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations of in New Caledonia.

Hen's teeth with enamel cap: from dream to impossibility

Directory of Open Access Journals (Sweden)

Girondot Marc

2008-09-01

Full Text Available Abstract Background The ability to form teeth was lost in an ancestor of all modern birds, approximately 100-80 million years ago. However, experiments in chicken have revealed that the oral epithelium can respond to inductive signals from mouse mesenchyme, leading to reactivation of the odontogenic pathway. Recently, tooth germs similar to crocodile rudimentary teeth were found in a chicken mutant. These "chicken teeth" did not develop further, but the question remains whether functional teeth with enamel cap would have been obtained if the experiments had been carried out over a longer time period or if the chicken mutants had survived. The next odontogenetic step would have been tooth differentiation, involving deposition of dental proteins. Results Using bioinformatics, we assessed the fate of the four dental proteins thought to be specific to enamel (amelogenin, AMEL; ameloblastin, AMBN; enamelin, ENAM and to dentin (dentin sialophosphoprotein, DSPP in the chicken genome. Conservation of gene synteny in amniotes allowed definition of target DNA regions in which we searched for sequence similarity. We found the full-length chicken AMEL and the only N-terminal region of DSPP, and both are invalidated genes. AMBN and ENAM disappeared after chromosomal rearrangements occurred in the candidate region in a bird ancestor. Conclusion These findings not only imply that functional teeth with enamel covering, as present in ancestral Aves, will never be obtained in birds, but they also indicate that these four protein genes were dental specific, at least in the last toothed ancestor of modern birds, a specificity which has been questioned in recent years.

Cenozoic climate change shaped the evolutionary ecophysiology of the Cupressaceae conifers.

Science.gov (United States)

Pittermann, Jarmila; Stuart, Stephanie A; Dawson, Todd E; Moreau, Astrid

2012-06-12

The Cupressaceae clade has the broadest diversity in habitat and morphology of any conifer family. This clade is characterized by highly divergent physiological strategies, with deciduous swamp-adapted genera-like Taxodium at one extreme, and evergreen desert genera-like Cupressus at the other. The size disparity within the Cupressaceae is equally impressive, with members ranging from 5-m-tall juniper shrubs to 100-m-tall redwood trees. Phylogenetic studies demonstrate that despite this variation, these taxa all share a single common ancestor; by extension, they also share a common ancestral habitat. Here, we use a common-garden approach to compare xylem and leaf-level physiology in this family. We then apply comparative phylogenetic methods to infer how Cenozoic climatic change shaped the morphological and physiological differences between modern-day members of the Cupressaceae. Our data show that drought-resistant crown clades (the Cupressoid and Callitroid clades) most likely evolved from drought-intolerant Mesozoic ancestors, and that this pattern is consistent with proposed shifts in post-Eocene paleoclimates. We also provide evidence that within the Cupressaceae, the evolution of drought-resistant xylem is coupled to increased carbon investment in xylem tissue, reduced xylem transport efficiency, and at the leaf level, reduced photosynthetic capacity. Phylogenetically based analyses suggest that the ancestors of the Cupressaceae were dependent upon moist habitats, and that drought-resistant physiology developed along with increasing habitat aridity from the Oligocene onward. We conclude that the modern biogeography of the Cupressaceae conifers was shaped in large part by their capacity to adapt to drought.

Enigmatic cranial superstructures among Chamorro ancestors from the Mariana Islands: gross anatomy and microanatomy.

Science.gov (United States)

Heathcote, Gary M; Bromage, Timothy G; Sava, Vincent J; Hanson, Douglas B; Anderson, Bruce E

2014-06-01

This study focuses on the gross anatomy, anatomic relations, microanatomy, and the meaning of three enigmatic, geographically patterned, and quasi-continuous superstructures of the posterior cranium. Collectively known as occipital superstructures (OSSs), these traits are the occipital torus tubercle (TOT), retromastoid process (PR), and posterior supramastoid tubercle (TSP). When present, TOT, PR, and TSP develop at posterior cranial attachment sites of the upper trapezius, superior oblique, and sternocleidomastoid muscles, respectively. Marked expression and co-occurrence of these OSSs are virtually circumscribed within Oceania and reach highest recorded frequencies in protohistoric Chamorros (CHamoru) of the Mariana Islands. Prior to undertaking scanning electron microscopy (SEM) work, our working multifactorial model for OSS development was that early-onset, long-term, and chronic activity-related microtrauma at enthesis sites led to exuberant reactive or reparative responses in a substantial minority of genetically predisposed (and mostly male) individuals. SEM imaging, however, reveals topographic patterning that questions, but does not negate, activity induction of these superstructures. Although OSSs appear macroscopically as relatively large and discrete phenomena, SEM findings reveal a unique, widespread, and seemingly systemic distribution of structures over the occipital surface that have the appearance of OSS microforms. Nevertheless, apparent genetic underpinnings, anatomic relationships with muscle entheses, and positive correlation of OSS development with humeral robusticity continue to suggest that these superstructures have potential to at once bear witness to Chamorro population history and inform osteobiographical constructions of chronic activity patterns in individuals bearing them. Further work is outlined that would illuminate the proximate and ultimate meanings of OSS. Copyright © 2014 Wiley Periodicals, Inc.

Integrated genomic and transcriptomic analysis reveals mycoparasitism as the ancestoral life style of Trichoderma

Energy Technology Data Exchange (ETDEWEB)

Kubicek, Christian P.; Herrera-Estrella, Alfredo; Seidl, Verena; Crom, St& #233; phane Le; Martinez, Diego A.; Druzhinina, Irina S.; Zeilinger, Susanne; Casas-Flores, Sergio; Horwitz, Benjamin A.; Mukherjee, Prasun K.; Mukherjee, Mala; Kredics, L& #225; szlo; Alcaraz, Luis David; Aerts, Andrea; Antal, Zsuzsanna; Atanasova, Lea; Cervantes-Badillo, Mayte Guadalupe; Challacombe, Jean; Chertkov, Olga; McCluskey, Kevin; Coulpier, Fanny; Deshpande, Nandan; D& #246; hren, Hans von; Ebbole, Daniel J.; Esquivel-Naranjo, Edgardo Ulises; Fekete, Erzs& #233; bet; Flipphi, Michel; Glaser, Fabian; Gomez-Rodriguez, Elida Yazmin; Gruber, Sabine; Han, Cliff; Henrissat, Bernard; Hermosa, Rosa; Hern& #225; ndez-O?ate, Miguel; Karaffa, Levente; Kosti, Idit; Lindquist, Erika; Lucas, Susan; L& #252; beck, Mette; L& #252; beck, Peter Stephensen; Margeot, Antoine; Metz, Benjamin; Misra, Monica; Nevalainen, Helena; Omann, Markus; Packer, Nicolle; Perrone, Giancarlo; Uresti-Rivera, Edith Elena; Salamov, Asaf; Schmoll, Monika; Seiboth, Bernhard; Shapiro, Harris; Sukno, Serenella; Tamayo-Ramos, Juan Antonio; Thon, Michael; Tisch, Doris; Wiest, Aric; Wilkinson, Heather H.; Zhang, Michael; Coutinho, Pedro M.; Kenerley, Charles M.; Monte, Enrique; Baker, Scott E.; Grigoriev, Igor V.

2011-04-29

Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.

Intravarietal polymorphisms reveal possible common ancestor of native Schinus terebinthifolius Raddi populations in Brazil.

Science.gov (United States)

Pinto, J V C; Crispim, B A; Vasconcelos, A A; Geelen, D; Grisolia, A B; Vieira, M C

2016-01-08

Schinus terebinthifolius Raddi is a perennial native from Atlantic forest. It is of high ecological plasticity and is used in traditional medicine. Based on promising reports concerning its bioactivity, it was included as a species of great interest for distribution through the National Health System. A number of agronomic studies to guide its crop production are therefore underway. This study examined diversity and phylogenetic relationships among native S. terebinthifolius populations from different Brazilian ecosystems: Cerrado; sandbanks; dense rainforest; and deciduous forest. The intergenic regions rpl20-5'rps12, trnH-psbA, and trnS-trnG were sequenced from cpDNA and aligned using BLASTn. There were few fragments for comparison in GenBank and so only region trnS-trnG was informative. There were variations among and within populations with intravarietal polymorphisms and three distinct haplotypes (HpSM, HpDDO, HpNE), once populations from NE (sandbanks and rainforest) clustered together. Sequences from HpSM, HpNE, and HpDDO returned greater similarity to haplotypes A (AY928398.1), B (AY928399.1), and C (AY928400.1), respectively. A network, built by median-joining among native haplotypes and 10 available on GenBank, revealed HpSM as the origin of all other haplogroups. HpDDO showed the most mutations and was closely related to haplogroups from Argentina. While this could indicate hybridization, we believe that the polymorphisms resulted from adaptation to events such as deforestation, fire, rising temperature, and seasonal drought during the transition from Atlantic forest to Cerrado. While more detailed phylogeographical studies are needed, these results indicate eligible groups for distinct climates as an important step for pre-breeding programs before field propagation.

Parallel female preferences for call duration in a diploid ancestor of an allotetraploid treefrog.

Science.gov (United States)

Bee, Mark A

2008-09-01

The gray treefrog species complex (Hyla chrysoscelis and H. versicolor) comprises a single allotetraploid species (H. versicolor) that arose multiple times from hybrid matings between an extant diploid species (H. chrysoscelis) and at least two other extinct diploid treefrogs. While previous studies have investigated female preferences for call duration in the tetraploid, we know little about these preferences in its putative diploid anscestors. Here, I report results from two-choice phonotaxis experiments investigating call duration preferences in H. chrysoscelis. Females preferred an average-length call over shorter-than-average calls (0.5-2.0 standard deviations [SD] below average), and they preferred longer-than-average calls over average or shorter-than-average calls if the difference in pulse number was at least 2.0 SD. When the amplitude of the longer alternative was attenuated by 6 dB, females still preferred an average-length call over a shorter-than-average call, but there was no preference for longer-than-average calls over an average call. In the presence of chorus noise, female preferences for both average and longer-than-average calls over shorter alternatives were weakened or reversed. Together, the results from this study reveal patterns of female preferences for call duration that are strikingly similar among two members of a species complex with a novel evolutionary history. In both species, female preferences are directional, nonlinear, and limited by environmental noise. Furthermore, these results also highlight the need for caution in studies of sexual selection when extrapolating from patterns of female preference obtained under ideal laboratory conditions to conclusions about how those preferences are expressed in the real world.

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

Directory of Open Access Journals (Sweden)

Nagy Ervin D

2012-09-01

Full Text Available Abstract Background Cultivated peanut (Arachis hypogaea is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.

Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors.

Science.gov (United States)

Sandoval, Jose R; Salazar-Granara, Alberto; Acosta, Oscar; Castillo-Herrera, Wilder; Fujita, Ricardo; Pena, Sergio D J; Santos, Fabricio R

2013-09-01

In order to investigate the underlying genetic structure and genomic ancestry proportions of Peruvian subpopulations, we analyzed 551 human samples of 25 localities from the Andean, Amazonian, and Coastal regions of Peru with a set of 40 ancestry informative insertion-deletion polymorphisms. Using genotypes of reference populations from different continents for comparison, our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry. Among populations from the Titicaca Lake islands of Taquile, Amantani, Anapia, and Uros, and the Yanque locality from the southern Peruvian Andes, there was no significant proportion of non-autochthonous genomes, indicating that their genetic background is effectively derived from the first settlers of South America. However, the Andean populations from San Marcos, Cajamarca, Characato and Chogo, and coastal populations from Lambayeque and Lima displayed a low but significant European ancestry proportion. Furthermore, Amazonian localities of Pucallpa, Lamas, Chachapoyas, and Andean localities of Ayacucho and Huancayo displayed intermediate levels of non-autochthonous ancestry, mostly from Europe. These results are in close agreement with the documented history of post-Columbian immigrations in Peru and with several reports suggesting a larger effective size of indigenous inhabitants during the formation of the current country's population.

Modelling vocal anatomy's significant effect on speech

NARCIS (Netherlands)

de Boer, B.

2010-01-01

This paper investigates the effect of larynx position on the articulatory abilities of a humanlike vocal tract. Previous work has investigated models that were built to resemble the anatomy of existing species or fossil ancestors. This has led to conflicting conclusions about the relation between

A trophic framework for animal origins

DEFF Research Database (Denmark)

Mills, D. B.; Canfield, D. E.

2017-01-01

Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsist...

Healing and coping with life within challenges of spiritual insecurity ...

African Journals Online (AJOL)

Spiritual insecurity among African Christians is a huge challenge. The insecurity among other things arises from African people's former traditional African ancestral world view of ancestral veneration. The ancestors promote or hinder African Christians' reliance on Christ because they have presupposedly acquired the ...

Evolutionary and biomedical insights from the rhesus macaque genome

DEFF Research Database (Denmark)

Gibbs, Richard A; Rogers, Jeffrey; Katze, Michael G

2007-01-01

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied...

A note on the periphrastic past in Afrikaans

NARCIS (Netherlands)

Zwart, Jan-Wouter

2018-01-01

The periphrastic past tense of Afrikaans, involving the auxiliary het, is compared with its ancestor construction in Dutch. I argue that the situation in Afrikaans provides support for the analysis of Germanic verb clusters in Zwart (2017), where periphrastic verb forms occupy cells in morphological

The Amborella Genome and the Evolution of Flowering Plants

DEFF Research Database (Denmark)

Albert, Victor A.; Barbazuk, W. Bradley; dePamphilis, Claude W.

2013-01-01

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella...

Transmutations in Masquerade Costumes and Performances: An ...

African Journals Online (AJOL)

Masquerades or spirit manifests are uniquely ritualistic. Masquerade performances in African culture are symbolizations; they represent not only the physical and continuous presence of the ancestors but also their luminal sense of justice and equity. Masquerade, derived from mask presupposes that somebody's identity is ...

The danger of misunderstanding 'culture'

African Journals Online (AJOL)

Eva Keller

2009-12-02

Dec 2, 2009 ... such as eating lemurs or bats or felling trees, taboos seem to provide a ... recounted the following myth: “The Creator asked the Malagasy whether they ... birth of a healthy child is a sign that the ancestors are satisfied and that ...

The Physiology of Phagocytosis in the Context of Mitochondrial Origin

NARCIS (Netherlands)

Martin, William F; Tielens, Aloysius G M; Mentel, Marek; Garg, Sriram G; Gould, Sven B

How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still

Accelerating XPath Evaluation in Any RDBMS

NARCIS (Netherlands)

Grust, Torsten; Kolaitis, P.; Franklin, M.J.; van Keulen, Maurice; Teubner, J.

This article is a proposal for a database index structure, the XPath accelerator, that has been specifically designed to support the evaluation of XPath path expressions. As such, the index is capable to support all XPath axes (including ancestor, following, preceding-sibling, descendant-or-self,

Taiwans multi-etniske samfund og den oprindelige befolknings postkoloniale situation eksemplificeret ved genindførelsen af traditionelle ritualer

DEFF Research Database (Denmark)

Rudolph, Michael

2012-01-01

Since the middle of the 1990s, traditionalist performances were on the rise in Taiwan. Generously subsidized by government bodies, aboriginal elites now not only publicly worshipped ancestor gods and enacted animal sacrifices in so called revitalized rituals, but also used these occasions to point...

The impact of 'anthropotechnology’ on human evolution

NARCIS (Netherlands)

Blad, S.

2010-01-01

From the time that they diverged from their common ancestor, chimpanzees and humans have had a very different evolutionary path. It seems obvious that the appearance of culture and technology has increasingly alienated humans from the path of natural selection that has informed chimpanzee evolution.

Reconstructing the early evolution of the fungi using a six gene phylogeny

NARCIS (Netherlands)

James, T.Y.; Kauff, F.; Schoch, C.L.; Matheny, P.B.; Hofstetter, V.; Cox, C.J.; Celio, G.; Gueidan, C.; Fraker, E.; Miadlikowska, J.; Lumbsch, H.T.; Rauhut, A.; Reeb, V.; Arnold, A.E.; Amtoft, A.; Stajich, J.E.; Hosaka, K.; Sung, G.H.; Johnson, D.; O'Rourke, B.; Binder, M.; Curtis, J.M.; Slot, J.C.; Wang, Z.; Wilson, A.W.; Schüßler, A.; Longcore, J.E.; O'Donnell, K.; Mozley-Standridge, S.; Porter, D.; Letcher, P.M.; Powell, M.J.; Taylor, J.W.; White, M.M.; Griffith, G.W.; Davies, D.R.; Sugiyama, J.; Rossman, A.Y.; Rogers, J.D.; Pfister, D.H.; Hewitt, D.; Hansen, K.; Hambleton, S.; Shoemaker, R.A.; Kohlmeyer, J.; Volkmann-Kohlmeyer, B.; Spotts, R.A.; Serdani, M.; Crous, P.W.; Hughes, K.W.; Matsuura, K.; Langer, E.; Langer, G.; Untereiner, W.A.; Lücking, R.; Büdel, B.; Geiser, D.M.; Aptroot, A.; Diederich, P.; Schmitt, I.; Schultz, M.; Yahr, R.; Hibbett, D.S.; Lutzoni, F.; McLaughlin, D.J.; Spatafora, J.W.; Vilgalys, R.

2006-01-01

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore

Redemption in Totality

DEFF Research Database (Denmark)

Munch, Anders V.

2010-01-01

Richard Wagner is in his music dramas, philosophy and cultural critique a common ancestor of both the art forms of avant-garde and totalitarianism. Figures such as the architect Peter Behrens and the illustrator Fidus demonstrates how unpredictable the barriers ar between Wagnerian cultivators of...

Fatty acid compositions of preterm and term colostrum, transitional and mature milks in a sub-Saharan population with high fish intakes

NARCIS (Netherlands)

Kuipers, Remko S.; Luxwolda, Martine F.; Dijck-Brouwer, D. A. Janneke; Muskiet, Frits A. J.

2012-01-01

Background: There are no data on the fatty acid (FA) compositions of preterm and term milks for sub-Saharan African populations with advancing lactation. However, it is generally acknowledged that our ancestors evolved in sub-Saharan East-Africa, where they inhabited the land-water ecosystems.

Registration of N6001 soybean germplasm with enhanced yield derived from Japanese cultivar Suzuyutaka

Science.gov (United States)

The genetic base of U.S. soybean (Glycine max (L.) Merr.) is relatively narrow, with Chinese ancestors providing most of the genetic base. Japanese lines have made relatively small contributions, suggesting that incorporation of novel Japanese genetics into USA breeding populations may aid soybean ...

Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection

DEFF Research Database (Denmark)

Hobolth, Asger; Dutheil, Julien; Hawks, John

2011-01-01

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent HMM framework. We find ILS present in ~1%...

Boule-like genes regulate male and female gametogenesis in the flatworm Macrostomum lignano

NARCIS (Netherlands)

Kuales, G.; De Mulder, K.; Glashauser, J.; Salvenmoser, W.; Takashima, S.; Hartenstein, V.; Berezikov, E.; Salzburger, W.; Ladurner, P.

2011-01-01

Members of the DAZ (Deleted in AZoospermia) gene family are important players in the process of gametogenesis and their dysregulation accounts for 10% of human male infertility. Boule, the ancestor of the family, is mainly involved in male meiosis in most organisms. With the exception of Drosophila

An Epistemological Analysis of the African Ontology of `Ancestral ...

African Journals Online (AJOL)

The paper explores the contemporary debate surrounding the idea of ancestral reincarnation in African society and philosophy. It analyzes various problem areas having to do with the physical and spiritual status of ancestors, their relationship with their societies of orientation, the philosophical contexts of their existence, ...

Dealing with death and disaster

NARCIS (Netherlands)

Veere, van der H.

2011-01-01

The triple disaster of earthquake, tsunami and nuclear fallout has done great damage. From the perspective of the ritual system and worldview, veneration of ancestors and ritual duties, the damage is even greater although hard to imagine for outsiders to the specifics of Japanese culture. This

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

Science.gov (United States)

2017-05-10

share a common ancestor and have inherent parent -child 106 relationships. Fortunately, as previous studies have suggested, analysis at the clonotype...survival 609 niches. Semin Immunol, 2008. 20(1): p. 49-58. 610 5. Kuraoka, M., et al., Complex Antigens Drive Permissive Clonal Selection in Germinal

Structure and function of the hearts of lizards and snakes

NARCIS (Netherlands)

Jensen, Bjarke; Moorman, Antoon F. M.; Wang, Tobias

2014-01-01

With approximately 7000 species, snakes and lizards, collectively known as squamates, are by far the most species-rich group of reptiles. It was from reptile-like ancestors that mammals and birds evolved and squamates can be viewed as phylogenetically positioned between them and fishes. Hence, their

Evaluation of genetic diversity between 27 banana cultivars (Musa ...

African Journals Online (AJOL)

Cultivated bananas (Musa spp.) are mostly diploid or triploid cultivars with various combinations of the A and B genomes inherited from their diploid ancestors Musa acuminata Colla. and Musa balbisiana. Colla. respectively. Random amplified polymorphic DNA (RAPD) markers were used to establish the relatedness of 27 ...

What can we infer about the origin of sex in early eukaryotes?

NARCIS (Netherlands)

Speijer, Dave

2016-01-01

Current analysis shows that the last eukaryotic common ancestor (LECA) was capable of full meiotic sex. The original eukaryotic life cycle can probably be described as clonal, interrupted by episodic sex triggered by external or internal stressors. The cycle could have started in a highly flexible

The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

DEFF Research Database (Denmark)

Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki

2016-01-01

the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

Succinct Dynamic Cardinal Trees with Constant Time Operations for Small Alphabet

DEFF Research Database (Denmark)

Davoodi, Pooya; Satti, Srinivasa Rao

2011-01-01

) bits and performs the following operations in O(1) time: parent, child(i), label-child(alpha), degree, subtree-size, preorder, is-ancestor(x), insert-leaf (alpha), delete-leaf(alpha). The update times are amortized. The space is close to the information theoretic lower bound. The operations...

Zoology: Molluscs All Beneath the Sun, One Shell, Two Shells, More, or None.

Science.gov (United States)

Sigwart, Julia D

2017-07-24

One great remaining problem in evolutionary biology is to understand which common ancestor could have given rise to descendants as different as giant squid and microscopic pea clams. Two new papers provide important insights into molluscan body plan disparity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

2009-01-05

Jan 5, 2009 ... Ancient metazoan organisms arose from unicellular eukaryotes that had billions of years of genetic evolution behind them. The transcription factor networks present in single-celled ancestors at the origin of the Metazoa (multicellular animals) were already capable of mediating the switching of the ...

Runs of homozygosity implicate autozygosity as a schizophrenia risk factor

DEFF Research Database (Denmark)

Keller, Matthew C; Simonson, Matthew A; Ripke, Stephan

2012-01-01

Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Her...

The anatomy of the king crab Hapalogaster mertensii Brandt, 1850 (Anomura: Paguroidea: Hapalogastridae): new insights into the evolutionary transformation of hermit crabs into king crabs

NARCIS (Netherlands)

Keiler, J.; Richter, S.; Wirkner, C.S.

2015-01-01

The emergence of king crabs from a hermit crab-like ancestor is one of the most curious events in decapod evolution. King crabs comprise two taxa, Lithodidae and Hapalogastridae, and while lithodids have formed the focus of various anatomical studies, the internal anatomy of hapalogastrids has never

Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

NARCIS (Netherlands)

Kamminga, Tjerko

2017-01-01

Mycoplasma hyopneumoniae (M. hyopneumoniae) is a bacterial pathogen that has evolved from a gram-positive ancestor and specifically colonizes the lower respiratory tract of pigs where it causes enzootic pneumonia and plays a major role in the development of respiratory disease

Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping

Science.gov (United States)

At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos primigenius taurus more adapted to temperate climates and the tropically adapted Bos primigenius indicus. Human selection exponentially...

Explanatory models of mental disorders and treatment practices ...

African Journals Online (AJOL)

Objective: Key Words: Explanatory models; Traditional healers; Mental illness; South AfricaIn many traditional belief systems in Africa, including South Africa, mental health problems may be attributed to the influence of ancestors or to bewitchment. Traditional healers are viewed as having the expertise to address these ...

High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

Science.gov (United States)

High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

Did Australopithecus and Homo co-exist

International Nuclear Information System (INIS)

Vogel, J.C.

1984-01-01

Uranium series isotope dating of the tufas at Taung/Buxton suggests a considerably younger age for the Taung child (Australopithecus africanus) than has hitherto been accepted. If this later date is confirmed, it will necessitate a re-think of the evolutionary tree of Man and his ancestors

The evolution of fungal epiphytes

NARCIS (Netherlands)

Hongsanan, S.; Sánchez-Ramírez, S.; Crous, P.W.; Ariyawansa, H.A.; Zhao, R.L.; Hyde, K.D.

2016-01-01

Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors

Inventing Homo gardarensis: Prestige, Pressure and Human Evolution in Interwar Scandinavia

DEFF Research Database (Denmark)

Kjærgaard, Peter C.

2014-01-01

In the 1920s there were still very few fossil human remains to support an evolutionary explanation of human origins. Nonetheless, evolution as an explanatory framework was widely accepted. This led to a search for ancestors in several continents with fierce international competition. With so litt...

Alternative Definitions of Hispanics: Consequences in a Alcohol Survey.

Science.gov (United States)

Caetano, Raul

1986-01-01

Examines impact of different definitions of Hispanic ethnicity on sociodemographic characteristics, drinking patterns, and rate of alcohol problems among 1,453 Hispanic-American respondents. Defines Hispanic ethnicity by ethnicity of family of origin, national group, country most ancestors came from, and birthplace. Finds major differences between…

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

Science.gov (United States)

Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

2013-01-01

Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI: http://dx.doi.org/10.7554/eLife.01102.001 PMID:24137540

And the Dead Remain Behind

Directory of Open Access Journals (Sweden)

Peter Read

2013-08-01

Full Text Available In most cultures the dead and their living relatives are held in a dialogic relationship. The dead have made it clear, while living, what they expect from their descendants. The living, for their part, wish to honour the tombs of their ancestors; at the least, to keep the graves of the recent dead from disrepair. Despite the strictures, the living can fail their responsibilities, for example, by migration to foreign countries. The peripatetic Chinese are one of the few cultures able to overcome the dilemma of the wanderer or the exile. With the help of a priest, an Australian Chinese migrant may summon the soul of an ancestor from an Asian grave to a Melbourne temple, where the spirit, though removed from its earthly vessel, will rest and remain at peace. Amongst cultures in which such practices are not culturally appropriate, to fail to honour the family dead can be exquisitely painful. Violence is the cause of most failure.

Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.

Science.gov (United States)

van Hooff, Jolien J E; Snel, Berend; Seidl, Michael F

2014-05-01

Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.

Ubiquitin Signaling: Extreme Conservation as a Source of Diversity

Directory of Open Access Journals (Sweden)

Alice Zuin

2014-07-01

Full Text Available Around 2 × 103–2.5 × 103 million years ago, a unicellular organism with radically novel features, ancestor of all eukaryotes, dwelt the earth. This organism, commonly referred as the last eukaryotic common ancestor, contained in its proteome the same functionally capable ubiquitin molecule that all eukaryotic species contain today. The fact that ubiquitin protein has virtually not changed during all eukaryotic evolution contrasts with the high expansion of the ubiquitin system, constituted by hundreds of enzymes, ubiquitin-interacting proteins, protein complexes, and cofactors. Interestingly, the simplest genetic arrangement encoding a fully-equipped ubiquitin signaling system is constituted by five genes organized in an operon-like cluster, and is found in archaea. How did ubiquitin achieve the status of central element in eukaryotic physiology? We analyze here the features of the ubiquitin molecule and the network that it conforms, and propose notions to explain the complexity of the ubiquitin signaling system in eukaryotic cells.

Did the notochord evolve from an ancient axial muscle? The axochord hypothesis.

Science.gov (United States)

Brunet, Thibaut; Lauri, Antonella; Arendt, Detlev

2015-08-01

The origin of the notochord is one of the key remaining mysteries of our evolutionary ancestry. Here, we present a multi-level comparison of the chordate notochord to the axochord, a paired axial muscle spanning the ventral midline of annelid worms and other invertebrates. At the cellular level, comparative molecular profiling in the marine annelids P. dumerilii and C. teleta reveals expression of similar, specific gene sets in presumptive axochordal and notochordal cells. These cells also occupy corresponding positions in a conserved anatomical topology and undergo similar morphogenetic movements. At the organ level, a detailed comparison of bilaterian musculatures reveals that most phyla form axochord-like muscles, suggesting that such a muscle was already present in urbilaterian ancestors. Integrating comparative evidence at the cell and organ level, we propose that the notochord evolved by modification of a ventromedian muscle followed by the assembly of an axial complex supporting swimming in vertebrate ancestors. © 2015 The Authors. Bioessays published by WILEY Periodicals, Inc.

Evolutionary relationships among self-incompatibility RNases

Science.gov (United States)

Igic, Boris; Kohn, Joshua R.

2001-01-01

T2-type RNases are responsible for self-pollen recognition and rejection in three distantly related families of flowering plants—the Solanaceae, Scrophulariaceae, and Rosaceae. We used phylogenetic analyses of 67 T2-type RNases together with information on intron number and position to determine whether the use of RNases for self-incompatibility in these families is homologous or convergent. All methods of phylogenetic reconstruction as well as patterns of variation in intron structure find that all self-incompatibility RNases along with non-S genes from only two taxa form a monophyletic clade. Several lines of evidence suggest that the best interpretation of this pattern is homology of self-incompatibility RNases from the Scrophulariaceae, Solanaceae, and Rosaceae. Because the most recent common ancestor of these three families is the ancestor of ≈75% of dicot families, our results indicate that RNase-based self-incompatibility was the ancestral state in the majority of dicots. PMID:11698683

Genetic variability in common wheat germplasm based on coefficients of parentage

Directory of Open Access Journals (Sweden)

Fernanda Bered

2002-01-01

Full Text Available The characterization of genetic variability and an estimate of the genetic relationship among varieties are essential to any breeding program, because artificial crosses among less similar parents allow a larger segregation and the combination of different favorable alleles. Genetic variability can be evaluated in different ways, including the Coefficient of Parentage (COP, which estimates the probability of two alleles in two different individuals being identical by descent. In this study, we evaluated the degree of genetic relationship among 53 wheat genotypes, and identified the ancestor genotypes which contributed the most to the current wheat germplasm, as a prediction of the width of the genetic base of this cereal. The results revealed a mean COP of 0.07 and the formation of 22 similarity groups. The ancestor genotypes Ciano 67 and Mentana were those which contributed the most to the current wheat germplasm. According to the COP analyses, the genetic base of wheat rests on a small number of ancestral genotypes.

Evolution Is Linear: Debunking Life's Little Joke.

Science.gov (United States)

Jenner, Ronald A

2018-01-01

Linear depictions of the evolutionary process are ubiquitous in popular culture, but linear evolutionary imagery is strongly rejected by scientists who argue that evolution branches. This point is frequently illustrated by saying that we didn't evolve from monkeys, but that we are related to them as collateral relatives. Yet, we did evolve from monkeys, but our monkey ancestors are extinct, not extant. Influential voices, such as the late Stephen Jay Gould, have misled audiences for decades by falsely portraying the linear and branching aspects of evolution to be in conflict, and by failing to distinguish between the legitimate linearity of evolutionary descent, and the branching relationships among collateral relatives that result when lineages of ancestors diverge. The purpose of this article is to correct the widespread misplaced rejection of linear evolutionary imagery, and to re-emphasize the basic truth that the evolutionary process is fundamentally linear. © 2017 WILEY Periodicals, Inc.

Human cranial diversity and evidence for an ancient lineage of modern humans.

Science.gov (United States)

Schillaci, Michael A

2008-06-01

This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76-100 ka).

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Science.gov (United States)

Porter, Ashleigh F; Duggan, Ana T; Poinar, Hendrik N; Holmes, Edward C

2017-09-28

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum

Directory of Open Access Journals (Sweden)

Ashleigh F. Porter

2017-09-01

Full Text Available The complete genome sequences of two strains of variola virus (VARV sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

Centrality determination using the Glauber model in Xe-Xe collisions at $\\sqrt{s_{\\rm NN}} = 5.44$ TeV

CERN Document Server

2018-01-01

This document describes the methods used by the ALICE Collaboration for determining the centrality of Xe-Xe collisions at $\\sqrt{s_{\\rm NN}} = 5.44$ TeV at the LHC within the Glauber model. The half-density radius $R$ and the diffusivity $a$ describing the Xe-129 nucleus with a 2-parameter Fermi distribution have been derived from a recent electron scattering measurement for the Xe-132 nucleus. The deformation parameter $\\beta$ has been derived by an interpolation between measured deformation parameters for the even-$A$ Xe isotopes. The inelastic nucleon-nucleon cross-section at $\\sqrt{s_{\\rm NN}} = 5.44$ TeV has been estimated by interpolation of pp data at different center-of-mass energies. The particle multiplicity per nucleon-nucleon collision has been parameterized by a negative binomial distribution (NBD) and a number of independently emitting sources (ancestors) given by a linear combination of $N_{\\rm part}$ and $N_{\\rm coll}$. The NBD parameters $\\mu$ and $k$ and the ancestor parameter $f$ are then...

CINÉCLUB

CERN Multimedia

CINÉCLUB

2013-01-01

Every Thursday at 20h00 Council Chamber, 503/1-001 PROGRAMME APRIL 2013 Cycle Sergueï Paradjanov 11th April Shadows of Forgotten Ancestors URSS, 1964, 92min Film director from the Soviet school and of Armenian origins, Sergei Parajanov presented Shadows of Forgotten Ancestors in 1964. This film brought him international recognition, but the Communist Party immediately blacklisted him. Not having made anything anti political or offensive towards the regime at all, his interests in small independent Ukrainian communities, and his iconoclast cinema rich in symbolism contrast with the socialist realism that is then strongly encouraged to cinema. Indeed, Soviet cinema, which rose in the 20's as a Marxist propaganda force, is encouraging understandable cinema for the masses and should abhor Western ideologies. Some few experimental exceptions, such as The Man with a Movie Camera (Dziga Vertov, 1929) and production from Mezhrabpom studios withstand, but these instances are quite seldom. In the ...

Molecular and cytogenetic characterization of a durum wheat Aegilops speltoides chromosome translocation conferring resistance to stem rust

Science.gov (United States)

Stem rust is a serious disease of wheat that has caused historical epidemics, but it has not been a threat in recent decades in North America due to the eradication of the alternate host and deployment of resistant cultivars. However, the recent emergence of Ug99 (or race TTKS) poses a threat to glo...

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats

DEFF Research Database (Denmark)

Thiagavel, Jeneni; Cechetto, Clément; Santana, Sharlene E

2018-01-01

and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation...

Luther's Antisemitism in Historical Context: A Necessary Discussion for Christian Educators

Science.gov (United States)

Lindquist, David H.

2013-01-01

Martin Luther remains a complex, contradictory figure whose impact on modern Western history cannot be overstated. Among the most controversial aspects of Luther's work is his ambivalent perspective of the Jews. The early Luther viewed the Jews warmly, depicting them as Christianity's historical and religious ancestors. Later, however, he…

Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut

Science.gov (United States)

Peanut (Arachis hypogaea; 2n=4x=40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. ...

Rice as commodity and anti-commodity

NARCIS (Netherlands)

Richards, P.

2016-01-01

On the Upper West Africa coast rice belongs to two species — African rice (Oryza glaberrima Steud.) and Asian rice (Oryza sativa L.). African rice was domesticated in the region, perhaps three millennia ago, from a presumed wild ancestor, O. barthii. Asian rice was introduced via trans-Saharan

The Theme of Beauty in Leopold Sedar Senghor's Poetry ...

African Journals Online (AJOL)

In his long and immensely successful career,1 Leopold Sedar Senghor celebrates the beauty of three major places or landmarks, namely, the African geographical landscape; the spirit and essence of womanhood, especially black womanhood; and the ethos of the dead ancestors. This essay is organized into three ...

Virus Diseases: The Global Challenge to Health for All. Asia-Pacific Congress of Medical Virology (2nd) Held in Bangkok, Thailand on November 17-22, 1991. Abstracts

Science.gov (United States)

1992-07-01

question. This procedure allows the comparison of strains which have no more than 10% sequence divergence. Analysis using the UPGMA method revealed...unweighted pair group method using arithmetic averages ( UPGMA ) indicates that CA24v had evolved from a common ancestor which appeared in one focal place in

Morpho-functional characterization of the systemic venous pole of the reptile heart

NARCIS (Netherlands)

Jensen, Bjarke; Vesterskov, Signe; Boukens, Bastiaan J.; Nielsen, Jan M.; Moorman, Antoon F. M.; Christoffels, Vincent M.; Wang, Tobias

2017-01-01

Mammals evolved from reptile-like ancestors, and while the mammalian heart is driven by a distinct sinus node, a sinus node is not apparent in reptiles. We characterized the myocardial systemic venous pole, the sinus venosus, in reptiles to identify the dominant pacemaker and to assess whether the

Investigating Tree Thinking & Ancestry with Cladograms

Science.gov (United States)

Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

2015-01-01

Interpreting cladograms is a key skill for biological literacy. In this lesson, students interpret cladograms based on familial relationships and language relationships to build their understanding of tree thinking and to construct a definition of "common ancestor." These skills can then be applied to a true biological cladogram.

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters

NARCIS (Netherlands)

Iersel, van L.J.J.; Kelk, S.M.; Rupp, R.; Huson, D.H.

2010-01-01

Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different

Nutritional contribution of plant foods to human diet in evolution

NARCIS (Netherlands)

Schnorr, Stephanie Laurel

2016-01-01

Diets and food are indisputably core facets of human society. The great apes still rely on plants to supply most of their nutritional needs. Humans, however consume a diet that is nearly unrecognizable from that of early hominin and human ancestors. While the virtues of plant foods are widely

Animal evolution: stiff or squishy notochord origins?

Science.gov (United States)

Hejnol, Andreas; Lowe, Christopher J

2014-12-01

The notochord is considered an evolutionary novelty and one of the defining characters of chordates. A new study of an annelid challenges this view and proposes an earlier evolutionary origin in the most recent common ancestor of chordates and annelids. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

NARCIS (Netherlands)

Pel, Herman J.; de Winde, Johannes H.; Archer, David B.; Dyer, Paul S.; Hofmann, Gerald; Schaap, Peter J.; Turner, Geoffrey; Albang, Richard; Albermann, Kaj; Andersen, Mikael R.; Bendtsen, Jannick D.; Benen, Jacques A. E.; van den Berg, Marco; Breestraat, Stefaan; Caddick, Mark X.; Contreras, Roland; Cornell, Michael; Coutinho, Pedro M.; Danchin, Etienne G. J.; Debets, Alfons J. M.; Dekker, Peter; van Dijck, Piet W. M.; van Dijk, Alard; Dijkhuizen, Lubbert; Driessen, Arnold J. M.; d'Enfert, Christophe; Geysens, Steven; Groot, Gert S. P.; de Groot, Piet W. J.; Guillemette, Thomas; Henrissat, Bernard; Herweijer, Marga; van den Hombergh, Johannes P. T. W.; van den Hondel, Cees A. M. J. J.; van der Heijden, Rene T. J. M.; van der Kaaij, Rachel M.; Klis, Frans M.; Kools, Harrie J.; Kubicek, Christian P.; van Kuyk, Patricia A.; Lauber, Juergen; Lu, Xin; van der Maarel, Marc J. E. C.; Meulenberg, Rogier; Menke, Hildegard; Mortimer, Martin A.; Nielsen, Jens; Oliver, Stephen G.; Olsthoorn, Maurien; Pal, Karoly; van Peij, Noel N. M. E.; Ram, Arthur F. J.; Rinas, Ursula; Roubos, Johannes A.; Sagt, Cees M. J.; Schmoll, Monika; Sun, Jibin; Ussery, David; Varga, Janos; Vervecken, Wouter; de Vondervoort, Peter J. J. van; Wedler, Holger; Wosten, Han A. B.; Zeng, An-Ping; van Ooyen, Albert J. J.; Visser, Jaap; Stam, Hein; Enfert, Christophe d’; Lauber, Jürgen; Goosen, Coenie; de Vries, Ronald P.

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of

A good son is sad if he hears the name of his father : the tabooing of names in China as a way of implementing social values

NARCIS (Netherlands)

Adamek, Piotr

2012-01-01

This dissertation deals with the tabooing of names in China, or bihui 避諱. The names of sovereigns, ancestors, officials, teachers, etc. were taboo, meaning that it was prohibited to pronounce or record them. This custom had an enormous impact on Chinese culture and serious consequences for the daily

The Igbo notion of the living dead as a critique of death in ...

African Journals Online (AJOL)

... overcomes the problem of nothingless of death as conceived in Heidegger's existentialism and therefore provides not only psychological assurance for the individual but also enhances social control and progress since man would always continue to be part of his community either as an ancestor or in a reincarnated form.

Understandings of Death and Dying for People of Chinese Origin

Science.gov (United States)

Hsu, Chiung-Yin; O'Connor, Margaret; Lee, Susan

2009-01-01

This article introduces the primary beliefs about ancestor worship, Taoism, Confucianism, Buddhism and traditional Chinese medicine that have influenced Chinese people for thousands of years, particularly in relation to death and dying. These cultures and traditions remain important for Chinese people wherever they live. Over a long period,…

Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution

Directory of Open Access Journals (Sweden)

Charleston W. K. Chiang

2016-05-01

Full Text Available Identity-by-descent (IBD is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to share an IBD segment if that segment is inherited from a recent shared common ancestor without intervening recombination. Segments several cM long can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample, and there are currently efforts to detect shorter segments from sequencing. Here, we study a problem of identifiability: because existing approaches detect IBD based on contiguous segments of identity-by-state, inferred long segments of IBD may arise from the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that significant proportions of inferred segments 1–2 cM long are results of conflations of two or more shorter segments, each at least 0.2 cM or longer, under demographic scenarios typical for modern humans for all programs tested. The impact of such conflation is much smaller for longer (> 2 cM segments. This biases the inferred IBD segment length distribution, and so can affect downstream inferences that depend on the assumption that each segment of IBD derives from a single common ancestor. As an example, we present and analyze an estimator of the de novo mutation rate using IBD segments, and demonstrate that unmodeled conflation leads to underestimates of the ages of the common ancestors on these segments, and hence a significant overestimate of the mutation rate. Understanding the conflation effect in detail will make its correction in future methods more tractable.

The unique deep sea—land connection: interactive 3D visualization and molecular phylogeny of Bathyhedyle boucheti n. sp. (Bathyhedylidae n. fam.—the first panpulmonate slug from bathyal zones

Directory of Open Access Journals (Sweden)

Timea P. Neusser

2016-12-01

Full Text Available The deep sea comprises vast unexplored areas and is expected to conceal significant undescribed invertebrate species diversity. Deep waters may act as a refuge for many relictual groups, including elusive and enigmatic higher taxa, but the evolutionary pathways by which colonization of the deep sea has occurred have scarcely been investigated. Sister group relationships between shallow water and deep sea taxa have been documented in several invertebrate groups, but are unknown between amphibious/terrestrial and deep-sea species. Here we describe in full and interactive 3D morphoanatomical detail the new sea slug species Bathyhedyle boucheti n. sp., dredged from the continental slope off Mozambique. Molecular and morphological analyses reveal that it represents a novel heterobranch gastropod lineage which we establish as the new family Bathyhedylidae. The family is robustly supported as sister to the recently discovered panpulmonate acochlidian family Aitengidae, which comprises amphibious species living along the sea shore as well as fully terrestrial species. This is the first marine-epibenthic representative among hedylopsacean Acochlidiida, the first record of an acochlidian from deep waters and the first documented panpulmonate deep-sea slug. Considering a marine mesopsammic ancestor, the external morphological features of Bathyhedyle n. gen. may be interpreted as independent adaptations to a benthic life style in the deep sea, including the large body size, broad foot and propodial tentacles. Alternatively, the common ancestor of Bathyhedylidae and Aitengidae may have been a macroscopic amphibious or even terrestrial species. We hypothesize that oophagy in the common ancestor of Aitengidae and Bathyhedylidae might explain the impressive ecological and evolutionary flexibility in habitat choice in the Acochlidiida.

Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage.

Science.gov (United States)

Bonito, Gregory; Smith, Matthew E; Nowak, Michael; Healy, Rosanne A; Guevara, Gonzalo; Cázares, Efren; Kinoshita, Akihiko; Nouhra, Eduardo R; Domínguez, Laura S; Tedersoo, Leho; Murat, Claude; Wang, Yun; Moreno, Baldomero Arroyo; Pfister, Donald H; Nara, Kazuhide; Zambonelli, Alessandra; Trappe, James M; Vilgalys, Rytas

2013-01-01

Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle

Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage.

Directory of Open Access Journals (Sweden)

Gregory Bonito

Full Text Available Truffles have evolved from epigeous (aboveground ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp. and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago, with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

Science.gov (United States)

Cardone, Maria Francesca; Jiang, Zhaoshi; D'Addabbo, Pietro; Archidiacono, Nicoletta; Rocchi, Mariano; Eichler, Evan E; Ventura, Mario

2008-01-01

Chromosomal rearrangements, such as translocations and inversions, are recurrent phenomena during evolution, and both of them are involved in reproductive isolation and speciation. To better understand the molecular basis of chromosome rearrangements and their part in karyotype evolution, we have investigated the history of human chromosome 17 by comparative fluorescence in situ hybridization (FISH) and sequence analysis. Human bacterial artificial chromosome/p1 artificial chromosome probes spanning the length of chromosome 17 were used in FISH experiments on great apes, Old World monkeys and New World monkeys to study the evolutionary history of this chromosome. We observed that the macaque marker order represents the ancestral organization. Human, chimpanzee and gorilla homologous chromosomes differ by a paracentric inversion that occurred specifically in the Homo sapiens/Pan troglodytes/Gorilla gorilla ancestor. Detailed analyses of the paracentric inversion revealed that the breakpoints mapped to two regions syntenic to human 17q12/21 and 17q23, both rich in segmental duplications. Sequence analyses of the human and macaque organization suggest that the duplication events occurred in the catarrhine ancestor with the duplication blocks continuing to duplicate or undergo gene conversion during evolution of the hominoid lineage. We propose that the presence of these duplicons has mediated the inversion in the H. sapiens/P. troglodytes/G. gorilla ancestor. Recently, the same duplication blocks have been shown to be polymorphic in the human population and to be involved in triggering microdeletion and duplication in human. These results further support a model where genomic architecture has a direct role in both rearrangement involved in karyotype evolution and genomic instability in human.

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.

Science.gov (United States)

Hsiang, Allison Y; Field, Daniel J; Webster, Timothy H; Behlke, Adam D B; Davis, Matthew B; Racicot, Rachel A; Gauthier, Jacques A

2015-05-20

The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K

Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

Science.gov (United States)

Klyosov, A A

2011-05-01

This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the

The Virtual Grand Tour as Educational Paradigm

DEFF Research Database (Denmark)

Hansen, Per Skafte; Mouritsen, Lars

2001-01-01

The Virtual Grand Tour as defined here bears some resemblance to its 18th century ancestor: a wide range of individual topics are treated as a whole; a tutor, whether real or simulated, present or remote, is provided; a set of problem solving tools forms an integrated part of the "traveller...

Photosynthesis: ancient, essential, complex, diverse ... and in need of improvement in a changing world

Science.gov (United States)

A challenge to crop improvement is the fact that the photosynthetic process has been fine tuned by billions of years of natural selection, and is subject to deeply rooted genetic controls shaped in the native environments of the crop ancestors. These may be difficult to change and may not be optima...

AFRREV IJAH, Vol.3 (1) January, 2014

African Journals Online (AJOL)

Toshiba

2014-01-09

Jan 9, 2014 ... Indexed African Journals Online: www.ajol.info. AFRREV IJAH ... What relates religion and environment, whether social or physical is ethics. This study .... companies, there were abundant animal and plant resources due to high soil ..... Also, it serves as the abode of ancestors and store place for historical.

The History of human impact on the genus Santalum in Hawai'i

Science.gov (United States)

Mark Merlin; Dan VanRavenswaay

1990-01-01

Adaptive radiation of Santalum in the Hawaiian archipelago has provided these remote islands with a number of endemic species and varieties. The prehistoric Polynesian inhabitants of Hawai'i utilized the sandalwood trees for many of the same traditional purposes as their South Pacific ancestors who had developed ethnobotanical relationships with...

Naturally occurred frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E avian leukosis virus infection in chicken

Science.gov (United States)

The group of highly related avian leukosis viruses (ALVs) in chickens were thought to have evolved from a common retroviral ancestor into six subgroups, A to E and J. These ALV subgroups use diverse cellular proteins encoded by four genetic loci in chickens as receptors to gain entry into host cells...

The Imagined Bear | Bieder | Current Writing: Text and Reception in ...

African Journals Online (AJOL)

This spiritual power was often articulated through stories such as those presented here where bears are portrayed as powerful sacred spirits; as ancestors, healers, shape-shifters, lovers and mates. The stories, however, are not just about bears; the stories are also about cultures and how peoplo saw themselves in bears ...

Evolution of the 2'-5'-Oligoadenylate Synthetase family in eukaryotes and bacteria

DEFF Research Database (Denmark)

Kjær, Karina Hansen; Poulsen, Jesper Buchhave; Reitamm, Tonu

2009-01-01

in bacteria that contains the five OAS-specific motifs. This indicates a specific relationship to OAS. The wide distribution of the OAS genes has made it possible to suggest how the OAS1 gene could have evolved from a common ancestor to choanoflagellates and metazoans. Furthermore, we suggest that the OASL...

On the origin of differentiation

Indian Academy of Sciences (India)

Unknown

a result of an adhesion mutation in a Chlamydomonas- like ancestor. For cellular slime moulds it could mean that gathering together cysts or spores in the soil is advantageous for dispersal and therefore encouraged by selection, and ultimately leading to aggregation by che- motaxis (Bonner 2003). Once multicellularity has ...

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

DEFF Research Database (Denmark)

Daetwyler, Hans D; Capitan, Aurélien; Pausch, Hubert

2014-01-01

The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes p...

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Science.gov (United States)

Natural selection has molded the evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos primigenius taurus more adapted to temperate climates and the tropically ad...

Genetic variation of white clover (Trifolium repens L.) collections ...

African Journals Online (AJOL)

STORAGESEVER

2010-05-24

May 24, 2010 ... incompatibility mechanism of disomic inheritance (Thomas,. 1987). In essence ..... Badr A, Sayed-Ahmed H, El-Shanshouri A, Watson LE (2002). Ancestors of white ... Caradus JR, Woodfield DR (1997). World checklist of ... within a natural population of white clover (Trifolium repense L). J. Ecol. 73: 615-624 ...

Introduction: people at work

NARCIS (Netherlands)

Peeters, M.C.W.; Jonge, de J.; Taris, A.W.; Peeters, M.; Jonge, de J.; Taris, T.

2014-01-01

For as long as mankind has existed, people have worked. Needless to say the nature of work has changed tremendously: our ancestors were mostly hunters and collectors, nowadays people work with data, ‘goods’ or other people, or provide services. What has not changed is that we still spend a

Fulltext PDF

Indian Academy of Sciences (India)

IAS Admin

116 Why Some Pool Shots are More Difficult Than Others. Justin Jankunas and Richard N Zare. 122 Some Physics Inside Drying Droplets. Dileep Mampallil. 135 From the Triangle Inequality to the Isoperimetric. Inequality. S Kesavan. 149 Seaweeds. Ancestors of Land Plants with Rich Diversity. Felix Bast. 116. 122. 149 ...

The evolution of the placenta drives a shift in sexual selection in livebearing fish

NARCIS (Netherlands)

Pollux, B.J.A.; Meredith, R.W.; Springer, M.S.; Garland, T.; Reznick, D.N.

2014-01-01

The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent–offspring conflicts during pregnancy1, 2, 3, 4. Theory predicts that the rise of these conflicts should drive a shift from a reliance on

Family Planning - A Priority Social and Health Action Programme for ...

African Journals Online (AJOL)

personal identity and value, make connections wich ancestors and descendants" ... which promote che use of safe and effective modern mechods of contraception which ... ety as a whole. FP services, on the other hand, are motivated ... you cannot fail to have noticed che almost total collapse of che economies of many ...

Learning the Structure of English by Means of Esperanto.

Science.gov (United States)

Jones, R. Kent

The Esperanto language was consciously designed as a coherent system, in contrast to the 3000 conventional languages originated by people's cave-dwelling ancestors. The systematic nature of Esperanto makes it ideal as an instructional tool. The amorphous nature of English makes its serious use very difficult for students. Even though they learn to…

Identity-by-descent mapping in a Scandinavian multiple sclerosis cohort

DEFF Research Database (Denmark)

Westerlind, Helga; Imrell, Kerstin; Ramanujam, Ryan

2015-01-01

ancestor and shared more frequently in case-case pairs. A total of 2106 MS patients of Nordic origin and 624 matched controls were genotyped on Illumina Human Quad 660 chip and an additional 1352 ethnically matched controls typed on Illumina HumanHap 550 and Illumina 1M were added. The quality control left...

Romancing the Zulu: H. Rider Haggard, Nada the Lily, and Salvage ...

African Journals Online (AJOL)

But there it is: a picture, as Lang says, 'of a dying people.' I hope that hundreds of years hence the highly educated descendants of the Zulu race may read it and learn therefrom something of the spirit of their own savage ancestors. (Haggard, The Days of My Life 2, 18) ...

Genetic studies on the South African Mutton Merino: growth traits

African Journals Online (AJOL)

Unknown

breed has undergone such a metamorphosis that it no longer bears much, if any, resemblance to its European ancestor. The need for a separate genetic characterization of this distinct South African strain is therefore evident. The aim of this study was to determine the applicable non-genetic factors and to estimate genetic ...

Indigenous knowledge, belief and practice of wild plants among the Meru of Kenya : past and present human-plant relations in East Africa

NARCIS (Netherlands)

Ibui, Alfreda Kajira

2007-01-01

Humankind has resulted to the wild for food and medication since prehistory. Kenya for instance has been named the Cradle of Humankind due to the many findings by the Leakey family, where it has been confirmed that most of our early ancestors were gatherers. While this could be seen as a phenomenon

the conservation of nature: more than just human survival to the zulu ...

African Journals Online (AJOL)

beautifully formulated by their ancestors through their profound observation and experience of natural resources. I have listed here some of these proverbs with their meanings. • ugwayi nehlaba = They are great friends. (Lit. it is tobacco and the aloe}. Said because snuff is rede of ground tobacco leaves and cold ash of dry.

A Manual of Cherokee Herbal Remedies: History, Information, Identification, Medicinal Healing.

Science.gov (United States)

Schafer, Patricia D.

This thesis reports on the research of 25 plants, used as herbal remedies since the 1800s by the author's Native American ancestors (the Day family) and the Cherokee tribe. The plants were identified in four state parks in southwestern Indiana. Information sources included the research literature, articles on Cherokee herbal remedies, and…

Prehistory: A Teacher's Guide. Education on Site.

Science.gov (United States)

Corbishley, Mike; Darvill, Tim; Stone, Peter

Chronologically prehistory accounts for over 99% of the human past. During this time, the earliest human ancestors spread across the world from Africa and changed, modified, and evolved until the species "Homo sapiens sapiens" made its appearance some 200,000 years ago. This teacher's guide provides an outline of the prehistory of the…

Innocent Onyewuenyi's “Philosophical re-appraisal of the African ...

African Journals Online (AJOL)

But whereas Onyewuenyi portrays the problem as being one of semantics, I shall in this paper argue that the challenge of explaining African cultural phenomenon is one of hermeneutics. The question is a question of hermeneutics, because its focus is not on whether ancestors are metaphysical entities, but rather on what ...

Resonance – Journal of Science Education | Indian Academy of ...

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education. Felix Bast. Articles written in Resonance – Journal of Science Education. Volume 19 Issue 2 February 2014 pp 149-159 General Article. Seaweeds: Ancestors of Land Plants with Rich Diversity · Felix Bast · More Details Fulltext PDF. Volume 20 Issue 4 April 2015 ...

The Australopithecines – An Extinct Group of Human Ancestors: My Scientific Interest in South Africa

Directory of Open Access Journals (Sweden)

Kaszycka Katarzyna A.

2017-06-01

Full Text Available I introduce the subject of my research interest in South Africa - the australopithecines - a group of bipedal, small-brained and large-toothed creatures from the Plio-Pleistocene, from which the human genus arose. I then briefly discuss various topics of my research, concerning: (1 Taxonomic status and morphological description of the extinct human relative from the Kromdraai site (Australopithecus robustus; (2 Graphic reconstruction of the partial skull from Kromdraai - specimen numbered TM 1517; (3 Assessment of size sexual dimorphism of the South African australopithecines (Australopithecus robustus and Australopithecus africanus, which, in terms of facial features, was pronounced - being almost gorilla-sized; (4 Social behavior of a fossil hominid species from around 2 million years ago, which, in terms of the social structure, was most likely a multimale-multifemale one; and (5 An event from the history of paleoanthropology, concerning the content of the 1924/25 photographs of the Taung Child (Australopithecus africanus - the first australopithecine skull discovered.

Ono Tupuna, the richness of the ancestors. Multiples Landscapes Relationalities in Contemporary Indigenous Rapa Nui

OpenAIRE

Rivas, Antonia

2017-01-01

Contemporary Rapa Nui is formed by a multiple and complex set of interactions, encounters, and circumstances that comprise the core of their indigenous identity, like many other indigenous people's realities. In this dissertation, I argue that there is not a simple or straightforward way of thinking about indigenous identities without falling into the trap of essentialism and stereotyping. Indigenous people are not what remained of ancestral civilizations, nor are they either invented nor fol...

Unruly grandmothers, ghosts and ancestors: Chinese elders and the importance of culture in dementia evaluations.

Science.gov (United States)

Elliott, Kathryn S; Di Minno, Mariann

2006-01-01

This article explores the cultural clashes that occurred when Chinese patients at an Alzheimer's center in California were evaluated for dementia. Lack of familiarity with Chinese culture made the culturally mainstream American clinicians at this center more likely to misinterpret the behavior of elderly Chinese-speaking patients and their families and, thereby, more likely to misdiagnose such patients and suggest culturally inappropriate recommendations. This tendency was reduced when relevant cultural knowledge was incorporated into the clinical evaluation. The evaluation process at this clinic and two patient examples are discussed to illustrate that familiarity with a patient's cultural background is essential for accurate diagnosis and referral. This ethnographic case study places the evaluation process in one particular clinic in cultural context and is suggestive in the way that exploratory qualitative research is meant to be, rather than broadly representative of dementia clinics or clinicians as a whole. However, problems created by cultural clashes at this clinic do suggest that what may be happening at other dementia clinics as they encounter increasingly more patients from diverse cultural backgrounds is an important empirical question worthy of further research, using both qualitative and quantitative methods.

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

DEFF Research Database (Denmark)

Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben

2013-01-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular...... evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae...... species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures...

Aerobic lineage of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic, (hyperthermophilic environment

Directory of Open Access Journals (Sweden)

Juan Pablo Cardenas

2016-11-01

Full Text Available Rubrerythrins (RBRs are non-heme di-iron proteins belonging to the ferritin-like superfamily (FLSF. They are involved in oxidative stress defense as peroxide scavengers in a wide range of organisms. The vast majority of RBRs, including classical forms of this protein, contain a C-terminal rubredoxin-like domain involved in electron transport that is used during catalysis in anaerobic conditions. Rubredoxin is an ancient and large protein family of short length (<100 residues that contains a Fe-S center involved in electron transfer. However, functional forms of the enzyme lacking the rubredoxin-like domain have been reported (e.g., sulerythrin and ferriperoxin. In this study, phylogenomic evidence is presented that suggests that a complete lineage of rubrerythrins, lacking the rubredoxin-like domain, arose in an ancient microaerobic and (hyperthermophilic environments in the ancestors of the Archaea Thermoproteales and Sulfolobales. This lineage (termed the aerobic-type lineage subsequently evolved to become adapted to environments with progressively lower temperatures and higher oxygen concentrations via the acquisition of two co-localized genes, termed DUF3501 and RFO, encoding a conserved protein of unknown function and a predicted Fe-S oxidoreductase respectively. Proposed Horizontal Gene Transfer (HGT events from these archaeal ancestors to Bacteria expanded the opportunities for further evolution of this RBR including adaption to lower temperatures. The second lineage (termed the cyanobacterial lineage is proposed to have evolved in cyanobacterial ancestors, maybe in direct response to the production of oxygen via oxygenic photosynthesis during the Great Oxygen Event (GOE. It is hypothesized that both lineages of RBR emerged in a largely anaerobic world with whiffs of oxygen and that their subsequent independent evolutionary trajectories allowed microorganisms to transition from this anaerobic world to an aerobic one.